[gmx-users] ligand topology

[Mohammad Zahidul Hossain Khan]

Dear Sir

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
>> my
>> 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
>
> --
> ==================================================
>
> 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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-- 


*Mohammad Zahidul Hossain Khan Graduate student**Department of Physics*
*Email: khan5121 at vandals.uidaho.edu <khan5121 at vandals.uidaho.edu>*
* Skype: parash.khan2*
*Cell: +12085967165*