[Dock-fans] solvgrid issue

Francesco Pietra chiendarret at gmail.com
Thu May 14 01:19:19 PDT 2009


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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