[gmx-users] adding ions in Gromacs 4.6.5

[Justin Lemkul]

On 11/19/14 4:33 AM, soumadwip ghosh wrote:
> Justin,
>             I have used the paramchem software as suggested by you. I
> submitted my pdb file and CGENFF gave a .str file as output. Now could you
> please tell me how to proceed to obtain the .itp file? Also is it sensible

Use our converter; it was designed to do this.

http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs

> to use SWISSPARAM since it gives .itp from .mol2 directly? Once I have the

I have never used SwissParam, I can only vouch for ParamChem.

> .itp file, I should include it to the .top file before adding the species
> via -ci and -nmol of genbox right?

Yes.

-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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