[gmx-users] SwissParam and Gromacs
jalemkul at vt.edu
Fri Dec 4 13:28:22 CET 2015
On 12/4/15 4:18 AM, Amali Guruge wrote:
> Dear All,
> I submitted docked conformation of topotecan molecule to the SwissParam
> server and I got itp file. Then I did a molecular dynamic simulation using
> that itp file (I used Gromacs software with CHARMM27 force field)
> When I tried to run the command,
> grompp -c b4em.pdb -f em01.mdp -n index.ndx -p system.top -o em01.tpr
> it gave the following error.
> *Fatal error:Atomtype CB not found*
> I attached the itp file received from the server. Please help me to correct
> this error.
This list does not accept attachments. You provided more significant
You said "After getting the itp file for the ligand, I used that file deleting [
atomtypes ] and [ pairtypes ]." You have deleted critical information.
SwissParam generates new atom types so that nothing conflicts with the parent
force field. By deleting them, you have rendered the ligand .itp file
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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