[gmx-users] ligand topology
Mohammad Zahidul Hossain Khan
za.parash at gmail.com
Tue Aug 1 01:17:26 CEST 2017
Thank you very much for your reply. Can you give me any link or suggestion
that i can learn for amber force field for protein and ligand.
On Mon, Jul 31, 2017 at 3:53 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> On 7/31/17 2:42 PM, Mohammad Zahidul Hossain Khan wrote:
>> Dear Sir
>> I am new for protein-ligand complex. I want amber force field (ff03) for
>> protein, tip3p for water model and gaff (General Amber force field) for
>> ligand. I do not know how to produce gaff force field from pdb and then
>> convert for gromacs topology.
>> I have tried ff03 with gromos ligand topology and tip3p water model
>> it gives me the error:
>> atomtype OM not found
>> and when I have tried ff03 with gromos topology and spc water model it
>> gives me the error like:
>> atomtype HW not found.
>> Can anyone help me about it?
> You can't mix and match force fields; it's fundamentally wrong. You need
> to develop ligand parameters that are consistent with the parent protein
> force field. Various tools exist for different force fields, with varying
> degrees of reliability.
> 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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*Mohammad Zahidul Hossain Khan Graduate student**Department of Physics*
*Email: khan5121 at vandals.uidaho.edu <khan5121 at vandals.uidaho.edu>*
* Skype: parash.khan2*
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