[gmx-users] Solvation causes failure of GROMPP preprocessing for Conjugate Gradients minimization?

[Mark Berjanskii]

Dear Gromacs users, 

Has anybody run into and found solution for a problem like the
following? 

When I try to pre-process input files for Conjugate Gradients
minimization of my protein in a box of water, grompp gives the following
error


ERROR: can not do Conjugate Gradients with constraints (12216)
There was 1 warning
Fatal error: There was 1 error

Gromacs exits after this error. 

I do not use any constraints or/and dummy atoms so the error does not
make sense to me. 

Interestingly, when I try to pre-process files for Conjugate Gradients
minimization of only protein, pre-procession runs just fine. So my guess
is that it is the protein solvation that causes the problem. 

Steepest descent preprocessing runs just fine.  

The command that I use to solvate protein is 
genbox -cp out -cs -p protein -o protein_water
(See output below.)

I use default water molecule. Changing the type of water molecule does
not help. 

The command for GROMPP script is 
grompp -v -f em.mdp -o full -c protein_water.gro -p protein
See output below. 

The MDP file (right below) I use for preprocessing is taken from Gromacs
demo. I changed only integrator from steep to sg.  

title               =  protein
cpp                 =  /lib/cpp
define              =  -DFLEX_SPC
constraints         =  none
integrator          =  cg
dt                  =  0.002    ; ps !
nsteps              =  10000
nstlist             =  10
ns_type             =  grid
rlist               =  1.0
rcoulomb            =  1.0
rvdw                =  1.0
;
;       Energy minimizing stuff
;
emtol               =  1000.0
emstep              =  0.01
nstcgsteep          =  1000



I use  Gromacs 3.2.1 on a computer with Red Hat 9.0 Linux OS.  

The was similar problem discussed before (see
http://www.gromacs.org/pipermail/gmx-users/2003-April/005280.html ) but
its solution is not applicable in my case because I do not use dummy
atoms (at least, intentionally).  

If anybody has an idea how to solve this mystery or/and have a working
example of mdp file for Conjugate Gradients minimization of a protein in
a water box, please let me know. 


Thank you, 

Mark Berjanskii
mberjans at bionmr.com
University of Alberta

P.S.

Below is output of Genbox and Grompp  runs. 

M.

****************************************************************************

"Useful" output of Genbox program: 

Opening library file /usr/local/gromacs/share/top/aminoacids.dat
Opening library file /usr/local/gromacs/share/top/atommass.dat
Opening library file /usr/local/gromacs/share/top/vdwradii.dat
Opening library file /usr/local/gromacs/share/top/dgsolv.dat
#Entries in atommass.dat: 82 vdwradii.dat: 26 dgsolv.dat: 7
Reading solute configuration
ETS-1; 5 SITE
Containing 1747 atoms in 110 residues
Initialising van der waals distances...
Reading solvent configuration
"216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984"
solvent configuration contains 648 atoms in 216 residues
 
Initialising van der waals distances...
Will generate new solvent configuration of 3x4x3 boxes
Generating configuration
Sorting configuration
Found 1 molecule type:
    SOL (   3 atoms):  7776 residues
Calculating Overlap...
box_margin = 0.315
Removed 6720 atoms that were outside the box
Table routines are used for coulomb: FALSE
Table routines are used for vdw:     FALSE
Cut-off's:   NS: 0.48   Coulomb: 0.48   LJ: 0.48
Generated table with 0 data points for COUL.
Tabscale = 500 points/nm
Generated table with 0 data points for LJ6.
Tabscale = 500 points/nm
Generated table with 0 data points for LJ12.
Tabscale = 500 points/nm
Going to determine what solvent types we have.
There are 0 molecules, 25075 charge groups and 25075 atoms
There are 0 optimized solvent molecules on node 0
There are 0 optimized water molecules on node 0
Grid: 20 x 27 x 18 cells
Succesfully made neighbourlist
nri = 38873, nrj = 1225795
Checking Protein-Solvent overlap: tested 39998 pairs, removed 1806
atoms.
Checking Solvent-Solvent overlap: tested 197195 pairs, removed 2586
atoms.
Added 4072 molecules
Generated solvent containing 12216 atoms in 4072 residues
Writing generated configuration to protein_water.gro
 
Back Off! I just backed up protein_water.gro to ./#protein_water.gro.4#
ETS-1; 5 SITE
 
Output configuration contains 13963 atoms in 4182 residues
Volume                 :     142.599 (nm^3)
Density                :      1000.3 (g/l)
Number of SOL molecules:   4072
 
Processing topology
 
Back Off! I just backed up protein.top to ./#protein.top.10#
 
gcq#51: "You Could Make More Money As a Butcher" (F. Zappa)
 
*****************************************************************



"Useful" output of Grompp 
 
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.34#
checking input for internal consistency...
calling /lib/cpp...
processing topology...
Generated 243951 of the 243951 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 243951 of the 243951 1-4 parameter combinations
Excluding 3 bonded neighbours for Protein 1
Excluding 2 bonded neighbours for SOL 4072
WARNING 1 [file "protein.top", line 16429]:
  System has non-zero total charge: -5.000000e+00
 
processing coordinates...
double-checking input for internal consistency...
ERROR: can not do Conjugate Gradients with constraints (12216)
There was 1 warning
Fatal error: There was 1 error

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