[gmx-users] $GMXLIB or the working directory

Justin Lemkul jalemkul at vt.edu
Thu Feb 4 13:53:19 CET 2016

Please continue this discussion on the gmx-users mailing list.  I am not a 
private help service.

On 2/4/16 12:13 AM, Mehreen Jan wrote:
> respected sir!
> thank so much for reply and time
> respected sir i have no idea about  whic kind of changes are required for $GMXLIB or the working directory
> i just make changes in  gromacs 4.5.5>share>top>gromacs43a1.ff . i have done no changes in $GMXLIB and i dont know what type of changes are / i required for $GMXLIB.
> snapshots are attached of all steps kindly find the attachment.
> step of command i performed :
> pdb2gmx -f protein.pdb -p protein.top -o protein.gro
> from list select the force field
> select 9    which is GROMOS96 32a1 force field
> select the water model:
> 1    SPC simple point charge
> then error message
> fatal error:
> residue SEP /TPO not found in residue topology database

Stop trying to modify 43A1; you likely aren't familiar enough with the structure 
and file formats.

Use the 43A1p files directly.  They work.  I verified it yesterday.  Download 
the force field archive, put it in your working directory or GMXLIB and use it. 
  Don't use 43A1 because it simply won't work.  This much should be clear based 
on the repetition of the exact same error message every time you do anything.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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