[gmx-users] Can I run an MD simulation without protein??

Scott Classen classen at uclink.berkeley.edu
Tue May 11 18:37:33 CEST 2004

Hello GROMAC Community,

I have a small molecule that I would like to do MD on (in a box full of 
DMSO), and I have used PRODRG to get a starting *.gro and *.itp file 
for my small molecule.

These are the commands I run and I have included part of my log file so 
that someone might be able to help me out.

 >editconf -f DRGFIN.GRO -o out.gro -bt tric -d 2 -box 2
 >genbox -cp out.gro -cs /programs/gromacs/share/top/dmso.gro -o 
 >grompp -f CDX-DMSO.mdp -c CDX-DMSO.gro -p CDX-topol.top -n 
CDX-DMSO.ndx -o CDX-DMSO.tpr

For the record my topology (CDX-topol.top) file looks like this:

;       File 'CDX-topol.top' was generated
;       By user: classen (7011)
;       On host: spry.Berkeley.EDU
;       At date: Mon May 10 17:45:40 2004
;       This is your topology file
;       "Right Now My Job is Eating These Doughnuts" (Bodycount)
; Include forcefield parameters
#include "ffgmx.itp"
#include "DRGGMX.ITP"
#include "/programs/gromacs/share/top/dmso.itp"
[ system ]
; Name
things n stuff
[ molecules ]
; Compound          #mols
CDX                 1
DMSO                 689

This is the end part of my log file. If you would like to see the whole 
thing I can post that also.
Thanks in advance for any help.

creating statusfile for 1 node...

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.4#
checking input for internal consistency...
calling /usr/bin/cpp...
processing topology...
Generated 1284 of the 1485 non-bonded parameter combinations
Excluding 3 bonded neighbours for CDX                 1
turning all bonds into constraints...
Excluding 2 bonded neighbours for DMSO                 689
turning all bonds into constraints...
WARNING 1 [file "CDX-topol.top", line 20]:
   System has non-zero total charge: -1.524016e-05

processing coordinates...
double-checking input for internal consistency...
Velocities were taken from a Maxwell distribution at 300 K
renumbering atomtypes...
converting bonded parameters...
#     ANGLES:   8396
#      PDIHS:   75
#      IDIHS:   3490
#       LJ14:   102
#     CONSTR:   6267
Walking down the molecule graph to make shake-blocks
initialising group options...
processing index file...
Fatal error: Group Protein not found in indexfile.
Maybe you have non-default goups in your mdp file, while not using the 
'-n' option of grompp.
In that case use the '-n' option.

   Scott Classen, Ph.D.
   ACS Postdoctoral Fellow
   Department of Molecular & Cell Biology
   University of California, Berkeley
   237 Hildebrand Hall #3206
   Berkeley, CA 94720-3206
   LAB 510.643.9491
   FAX 510.643.9290

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