C ============================================================= C GEPOL93 (GEometria POLihedro,1993) C Version 8 C Burjassot September 17, 1993. C ============================================================= C*** Written by C C J.L. Pascual-Ahuir, E. Silla and I. Tunon C Departamento de Quimica Fisica. C Facultad de Quimica. C Universidad de Valencia. C C/Dr.Moliner 50. C Burjassot (Valencia) 46100 C SPAIN C C Phone number: (34)-6-3864332 C FAX number: (34)-6-3864564 C EMAIL PASCUAL@EVALUN11 C SILLA@EVALUN11 C C*** Grants C C A grant has been provided by the Spanish Direccion General de C Investigacion Cientifica Y Tecnica (DGICYT), project PS 90-0264. C C*** OLD VERSIONS C C - GEPOL87 by J.L. Pascual-Ahuir, E. Silla, J. Tomasi and R. Bonacorsi C - GEPOL92 by J.L. Pascual-Ahuir, E. Silla and I. Tunon. C C*** Modifications with respect to GEPOL92 C The modifications affect mainly the computation of the Solvent- C Excluding Surface (ESURF). There are important changes in the C algorithm of the computation of the ESURF. The set of parameters C used for that computation is different from the old versions. C The computation of the surfaces of large systems as proteins, C with the old versions, takes a lot of time. With GEPOL93 this C problem has been solved. For a clear description of the new C algorithm see reference D. C C*** References C (Basic references) C C A- J.L.Pascual-Ahuir, E.Silla, J.Tomasi y R.Bonacorsi. C Electrostatic Interaction of Solute with a Continuum. C Improved Description of the Cavity and of the Surface Cavity C Bound Charge Distribution. C J. Comput. Chem.,8(1987)778-787 C C B- J. L. Pascual-Ahuir and E. Silla C GEPOL: An improved description of molecular surfaces. I. Building C the spherical surface set. C J. Comput. Chem.,11(1990)1047-1060 C C C- E. Silla, I. Tunon and J. L. Pascual-Ahuir C GEPOL: An improved description of molecular surfaces. II. Computing C the molecular area and volume. C J. Comput. Chem.,12(1991)1077-1088 C C D- J. L. Pascual-Ahuir, I Tunon and E. Silla C GEPOL: An improved description of molecular surfaces. III. A New C algorithm for the computation of the Solvent-Excluding Surface. C (explain the algorithm used in GEPOL93) C To be submited to J. Comput. Chem. during 1993 C C (References with examples of use) C C C E- J. L. Pascual-Ahuir and E. Silla C GEPOL: A method to calculate the envelope surface. Computation C of changes in conformational area and volume of n-octanol C Quantum Chemistry - Basics Aspects, Actual Trends. Ed. R. Carbo. C Studies in Physical and Theoretical Chemistry,62(1989)597-603 C Elsevier Science Publishers B. V., Amsterdam 1989. p C C F- J. L. Pascual-Ahuir, J. Andres and E. Silla. C Calculations of the relative basicities of methylamines in C solution C Chem. Phys. Lett., 169(1990)297-300 C C G- E. Silla, F. Villar, O. Nilsson, J.L. Pascual-Ahuir and O. Tapia. C Molecular volumes and surfaces of biomacromolecules via GEPOL: A C fast and efficient algorithm C J. Mol. Graphics,8(1990)168-172 C C H- F. M. Floris, J. Tomasi, J.L. Pascual-Ahuir C Dispersion and repulsion contributions to the solvation energy: C Refinements to a simple computational model in the continuum C Approximation. C J. Comput. Chem.,12(1991)784-791 C C I- I. Tunon, E. Silla and J. L. Pascual-Ahuir C Molecular surface area and hydrophobic effect C Protein Eng.,5(1992)715-716 C C J- I. Tunon, E. Silla and J. L. Pascual-Ahuir C Continuum-uniform approach calculations of the solubility C of hydrocarbons in water C Chem. Phys. Lett., 203(1993)289-294 C C K- I. Tunon, E. Silla and J. L. Pascual-Ahuir C Theoretical study of the inversion of the alcohol acidity C scale in aqueous solution. Toward an interpretation of the C acid-base behavior of organic compounds in solution. C J. Am. Chem. Soc. 115(1993)2226-2230 C C*** Aim C C This program computes the surface for a molecule as a distribution C of points and calculates its area and the volume enclosed. Each C point represents a piece of the surface named a tesserae. C C Three kinds of envelope surfaces can be computed: C C - THE VAN DER WAALS MOLECULAR SURFACE. This is the envelope C surface of a set of intersecting spheres with given atomic radii C centered on the nuclei of selected atoms of the molecule. C C - THE ACCESSIBLE MOLECULAR SURFACE. This was defined by C B.Lee and F.M.Richards (J.MOL.BIOL.55(1971)379-400). It is the C surface defined by the center of the solvent, considered as a C rigid sphere (probe sphere), when it rolls around the van der C Waals surface. C C - THE SOLVENT-EXCLUDING SURFACE. This is the surface envelope C of the volume excluded to the solvent, considered as a rigid C sphere (probe sphere), when it rolls around the van der Waals C surface. It was defined initially by F. M. Richards and named C as the MOLECULAR SURFACE (Ann. Rev. Biophys. Bioeng.,6 (1977) C 151-176) C GEPOL constructs the SOLVENT-EXCLUDING SURFACE creating a C set of new spheres located among the original spheres defined in C the input geometry. C C C*** Computacional especifications C C This program is written in FORTRAN 77 and has been run on C VAX (VMS) C SILICON GRAPHICS (UNIX) C IBM RISC (AIX) C C*** Input C C GENERAL INPUT (FOR005) C ---------------------- C This file will have the commands and parameters that control C the program. C Every record is a command and it is divided in two fields:The first C five characters of the field form a KEYWORD.The second field is C reserved for parameters. C You do not need to put the commands in a given order. C There are two types of KEYWORD depending on whether a parameter C is needed in the second field of the record or not. Those that need C a parameter have the symbol equal(=) included in the KEYWORD. C Every command has a default defined within the program. The default C values for the parameters are selected to achieve a good compromise C between time and accuracy. C C Each KEYWORD is explained, as follows: C C C TITL= This Keyword denotes that the title of the calculation goes C into the second field of the record. You may use up to 20 C records as titles, but each record should start with the C keyword TITL=.If you do not use this command the program C will provide a title. C C WSURF The van der Waals molecular surface is calculated. C C ASURF The accessible molecular surface is calculated. C C ESURF The Solvent-Excluding Surface (Molecular Surface) is C calculated. C C ( if you do not put in any of the latter keywords C the program will calculate the van der Waals surface) C C NDIV= In the second field goes an integer that can take values C between 1 and 5. It specifies the division level for the C triangles on the surface. The accuracy of the calculation C improves as NDIV rises. The default for this command is 3. C C OFAC= This parameter will be used only if ESURF is computed. C In the second field goes a real number that can take values C between 0.0 and 1.0. This parameter is the Overlapping FACtor. C The accuracy improves as the OFAC value increases.The default C value is 0.8 C C RMIN= This parameter will be used only if ESURF is computed. C In the second field goes a real number that can take values C larger than 0.0. This parameter is the radius of the smallest C sphere that can be created.The accuracy improves as the RMIN C value decreases.The default value is 0.50. C C (OFAC,RMIN are the parameters that control the creation C of new spheres) C C RSOL= This parameter will be used only if ASURF or ESURF is computed. C In the second field goes a real number. It is the probe or C solvent radius. The default value is 1.4 C C COOF= In the second field goes the name of the file with the C coordinates and radii. C C SPHF= The area of every sphere will be printed in the file C indicated in the second field. As default, the area of every C sphere will not be printed. For more information see later. C C VECF= The coordinates of the points, the components of the vectors C perpendicular to the surface and the areas of every tesserae, C will be printed in the file indicated in the second field. C As default the information will not be printed.The file C is written in binary format. C C DVEC= Only if you have selected VECF=. The number in the second C field gives the direction of the vectors and their module. C If the number is positive they will go outward and if it C is negative inward. The module of the vectors will be equal C to the absolutevalue of the number. As default the value C is +1. C C DISF= This option prints, in the file indicated in the second field, C information needed for a program, developed in our laboratory, C named HELIOS, that displays the surfaces. As default the C information is not printed. The file is written in binary C format. C C REDUC Only if SPHF= has been selected. The use of this command C will REDUCe the printing, giving only information about the C initial spheres. This option only has sense when the ESURF C is computed. C C ASSG1 Only if ESURF has been selected. This command assigns C the tesserae of the new spheres to the initial ones. C Thus the value of the area of each initial sphere will be C the sum of the area of the tesserae of itself plus the area C of the tesserae, from the new spheres, assigned to it. C A tesserae is assigned to the sphere whose surface is closest C to the tesserae. C As DEFAULT no assignation is made. C C LPRIN This command produce a longer printing in the general output. C As default a shorter printing is made C C C COORDINATES FILE C ---------------- C C The name of this file has been given in the general input after C the keyword COOF=. The format of the file is given next: C C -- TITLE C You can put in as many records of titles as you want, but each C record should start with the symbol *. C C -- NATOM (I8) C Number of atoms C C -- One record per atom (4F10.5,A33) C The Variables in each record are: C C XE Coordinate X of the atom. C YE Coordinate Y of the atom. C ZE Coordinate Z of the atom. C RE Radius of the sphere centered on the atom. C LABEL Atom number, atom name, residue number... This C variable is not used in GEPOL93, it is only read to C be written in the file SPHF= to identify each atom. C C OBSERVATIONS!!. C - With GEPOL93 we provide a program named PGEPOL that prepares C this file from others formats (PDB,GROMOS,CHARMM...) C - If you give a value to RE of 0.00000 this atom will not C participate at all in the calculation. C - If you give a negative value to RE this atom will have a C GHOST sphere. Sometimes we are interested only in computing C the surface of part of a molecule, but taking into account C the presence of the rest of the molecule. Thus, those atoms C that belong to the part of the molecule, which interests us, C will have positive RE and the rest of the atoms will have C their proper radii but negative. C - We are developing a set of programs to analyze the output of C GEPOL that makes use of the variable LABEL with a specific C format and information. If you are interested in using these C programs the format and information of LABEL should be the C following: C (I8,1x,A4,I7,1x,A4,I3,1x,A4) C IAT Atom number(order) C ATN Atom name C IRE Residue number(order) C REN Residue name C ISE Molecule number C SEN Molecule name C C C*** Output files C - The general output is connected to the fortran unit FOR006 C C - Information about the spheres C ----------------------------- C The name of this file is given after the keyword SPHF=. It contains C information about every sphere. C C -- TITLE (A80) C The same lines that were read in the coordinates file. C C -- NATOM (I8) C Number of atoms C C -- One record by atom or sphere (4F10.5,A33,F10.5) C The Variables in each record are: C C XE Coordinate X of the atom(center). C YE Coordinate Y of the atom. C ZE Coordinate Z of the atom. C RE Radius of the sphere centred on the atom. C LABEL Atom number, atom name, residue number... C AE Surface Area of this atom or sphere C C OBSERVATIONS!! C - If you have used REDUC you will get only information about the C original spheres. C C - Information about the tesserae forming the surface. C --------------------------------------------------- C The name of this file is given after the keyword VECF=. It contains C the coordinates of the center of each tesserae, the vectors C perpendicular to the surface at this point, the area of each tesserae. C It is written in binary format. The records have the following C information: C Record 1. LT (Integer*4) is the number of title record C Next LT rec. TITLE (charac.*80) title C Rec. LT+2 NP (Integer*4) Number of tesserae or points. C Next NP rec. (3integer*4,7real*4) each record has the C following variables: C C ITO each sphere can have up to 60 tesserae, ITO gives C the order number of this tesserae among the 60. C ISO gives the sphere number where the point lies. C ISA gives the sphere number assigned to this point C XP coordinate x of the point(center of the tesserae) C YP coordinate y of the point C ZP coordinate z of the point C AP area of the tesserae C XVEC component X of the vector C YVEC component Y of the vector C ZVEC component Z of the vector C C*** UNITS C The units of the area and volume will depend on the units of your C coordinates. Remember that XE,YE,ZE,RE,RSOL and RMIN should have C the same units. Thus if you use Angstroms the area will appear C in Angstroms**2 and the volume in Angstrom**3 C C*** Other information C This information may be useful if you want to add something to the C program. C MC = Maximum number of Centers (atoms, spheres) C MV = Maximum number of Vectors (points/tesserae) C IUSE(I) indicates the type of the center I C IUSE=1 Initial center with radius=0 (Set in Sub. READCOOR) C IUSE=2 Sphere engulfed by another (Set in Sub. CREA and BULK) C IUSE=3 Ghost sphere (Set in Sub. READCOOR) C IUSE=4 Sphere with final area 0 (Set in Sub. MZERO5 ) C IUSE=5 Semi ghost sphere (Set in Sub. SHELL ) C IUSE=6 Real sphere (Set in Sub. READCOOR) C***Problems C If you have any problems or suggestions, please do not hesitate to C contact us. C***************************************************************************