[gmx-users] Swissparam itp file

[Justin Lemkul]

On 6/24/15 7:19 AM, neha bharti wrote:
> Hello all
>
> I am trying to perform molecular dynamics simulation of ligand-protein
> complex in popc lipid with charmm36 force field. I am taking help from Justin
> A. Lemkul tutorial.
>
> First I perform orientation of protein ligand complex by following command:
>
> editconf -princ -f complex.gro -o complex_princ.gro
> editconf -rotate 0 90 0 -f complex_princ.gro -o complex_princ_rotate.gro
>
> Then after I separated the protein and ligand to generate their topology
> file.
> For protein pdb2gmx command is used for topology generation.
> For ligand topology file swissparam is used after adding the hydrogen and
> converting it to mol2 format.
>
> But from swissparam I only get the .par and .rtf file in zip folder and
> .itp is not persent. how to solve this issue??
>
> Although when I use the ligand molecule without orientation (without
> performing editconf -princ and editconf -rotate command) swissparam gives
> the .itp file.
> Can I use this itp file for oriented ligand molecule??
>

The topology is not dependent upon orientation.

-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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