[Dock-fans] Fwd: solvgrid issue

Francesco Pietra chiendarret at gmail.com
Thu May 14 02:22:57 PDT 2009


As last resource i tried by reducing the box size. Now the error in
running "solvgrid" was ;

At line 139 of file chemgrid.f (unit = 1, file = 'INRDSL')
Fortran runtime error: Bad real number in item 1 of list input



Line 139 in chemgrid.f of /solvgrids is "read(1,*) ... below


c
      grdcut=int(cutoff/grddiv + 1.0)
      read (1, *) pcon, ccon
      write (2, *) 'distances defining bumps with receptor atoms:'
      write (2, '(A21, F5.2)') 'receptor polar atoms ', pcon
      write (2, '(A22, F5.2)') 'receptor carbon atoms ', ccon
      pconsq=pcon*pcon
      cconsq=ccon*ccon
      read (1, 1000) grdfil
      write (2, *) 'output grid prefix name:'
      write (2, 1000) grdfil


The list input was:

/home/francesco/work/chemgrid/rec.pdb
/usr/local/dock6/parameters/chemgrid/prot.table.ambcrg.ambH
/usr/local/dock6/parameters/chemgrid/vdw.parms.amb.mindock
/home/francesco/work/chemgrid/box2236.margin0.pdb
0.33
1
4
2.3,2.8
solvgrid
sol_op
solE_recep





---------- Forwarded message ----------
From: Francesco Pietra <chiendarret at gmail.com>
Date: Thu, May 14, 2009 at 10:19 AM
Subject: solvgrid issue
To: dock-fans <dock-fans at docking.org>


Hi (addressed to those who may know):

With dock6.2 solvgrid INRDSL file

receptor.pdb ; receptor pdb file
parameters/ prot.table.ambcrg.ambH ; charge parameter file
parameters/ vdw.parms.amb.mindock ; VDW parameter file
box.pdb ; box pdb file
0.33 ; grid spacing in angstroms
1 ; es type: distance-dependent dielectric; 2: constant dielectric
4 ; es scale for ff scoring
2.3 2.8 ; bumping distances for polar and non-polar receptor atoms
output_prefix ; output grid prefix name
sol_op ; method for calculating desolvation grid
solE_recep; solvation free energy of receptor

i systematically get "max nr of grid points exceeded". What I tried:


---- Increased maxpts from default 10,000,000 to 100,000,000 (with
1000,000,000 dock6.2 does not compile) in chemgrid.h of chemgrids

--- Additionally changed perang in solvmap.f

c  perang: number of grid points per angstrom
      real invgrid
c  invgrid: inverse of perang
      integer n(2), il, ierr

from previous (3)

at no avail. Same grid points exceeded.


Changing "0.33" is INRDSL was not accepted; Fortran error.

===

If maxpts is increased to 1000,000,000 compilation fails. It fails
also if maxpts is increased to 100,000,000 in chemgrid.h of both
/chemgrids and /solvgrid.
========

In this badly documented section of dock6.2 manual i could
indefinitely go on by trial and error. Hope someone knows and
discloses his knowledge in explicit terms.

thanks
francesco pietra


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