[gmx-users] ligand topology

[Justin Lemkul]

On 8/1/17 2:23 PM, Lucio Ricardo Montero Valenzuela wrote:
> Ok, you should not mix and match forcefields, ¿but in the case of AMBER99SB for the protein and gaff for ligand? (TIP3P wáter).

GAFF is compatible with AMBER (by design).  My comments were warning that one 
should not use AMBER for a protein in concert with GROMOS for a ligand.

-Justin

> Best regards.
> Lucio Montero.
> 
> Enviado desde Correo para Windows 10
> 
> De: Alan
> Enviado: martes, 1 de agosto de 2017 11:01 a. m.
> Para: Gromacs
> Asunto: Re: [gmx-users] ligand topology
> 
> Please this GitHub link is totally outdated and not linked in any sense to
> the original authors.
> 
> Get the correct ACPYPE here:
> 
> svn checkout http://ccpn.svn.sourceforge.net/svnroot/ccpn/branches/
> stable/ccpn/python/acpype acpype
> 
> On 1 August 2017 at 15:00, Suhaib Shekfeh <s.shekfeh at gmail.com> wrote:
> 
>> Actually, GAFF forcefield and amber forcefields are compatible. gaff is
>> simply amber ff for small molecules.
>> You have to get first amber tools. The last release is amber tools 16
>> Get the source code from here :
>> http://ambermd.org/AmberTools16-get.html
>>
>> after installation you can use antechamber for creating the small-molecule
>> parameters
>>
>> later, you can use a nice free program called ACEPYP, made to convert amber
>> parameters to gromacs toplogyget the code from here:
>>
>> https://github.com/t-/acpype
>>
>> Regards
>>
>>
>>
>> On Tue, Aug 1, 2017 at 1:17 AM, Mohammad Zahidul Hossain Khan <
>> za.parash at gmail.com> wrote:
>>
>>> 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
>>>>
>>>> ==================================================
>>>> --
>>>> Gromacs Users mailing list
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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*
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>>
>>
>>
>> --
>> Dr. rer. nat. Suhaib Shekfeh
>> PhD in Computational Drug Design and Medicinal Chemistry
>> Oleariusstr. 11, Halle (Saale), Germany
>> LinkedIn : http://www.linkedin.com/pub/suhaib-shekfeh/b/65a/255
>> --
>> Gromacs Users mailing list
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> 
> 
> 

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

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

==================================================