[gmx-users] SwissParam and Gromacs

[Justin Lemkul]

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 
information here:

https://www.researchgate.net/post/How_can_I_use_the_itp_file_generated_from_SwissParm_for_MD_simulation_using_GROMACS

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 
nonfunctional.

-Justin

-- 
==================================================

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
http://mackerell.umaryland.edu/~jalemkul

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