On 12/1/13 9:51 PM, rdwducl wrote:

I am trying to use implicit solvation but I am getting the following error
from the preprocessor:

Program grompp_mpi, VERSION 4.6.4
Source code file:
/home/robert/Research/Software/gromacs-4.6.4/src/kernel/topio.c, line: 734

Fatal error:
Syntax error - File gbsa.itp, line 1
Last line read:
'[ implicit_genborn_params ]'
Invalid order for directive implicit_genborn_params
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

My topology file:

#include "ffG45a3.itp"
#include "cta.itp"
#include "ions.itp"
#include "gbsa.itp"

[ system ]
CTAC micelle implicit

[ molecules ]
CTA        80
CL-        80

The #includes are pretty self-explanatory but here is the head of gbsa.itp:

[ implicit_genborn_params ]
C16 1.0 1 1.0 0.207 1.0
C15 1.0 1 1.0 0.207 1.0
C14 1.0 1 1.0 0.207 1.0

I have read the manual regarding the order of directives in the topology
file but that hasn't helped me.

Perhaps I'm just tired. Can anyone see the problem?

All force field-level directives must be #included before any molecule-level directives (e.g. [moleculetype]) can be declared. Think of it this way: you have to define all of the parameters of all of the atom types before any of those types can be used within molecules. Therefore, gbsa.itp must be #included second in the list.



Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

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