[gmx-users] ligand topology

Tue Aug 1 23:18:55 CEST 2017

Dear Sir

I have just use acpype.py -i OAI.pdb
I am getting the error:
ERROR: no 'antechamber' executable!
ERROR: no 'antechamber' executable... aborting !
==> HINT1: is 'AMBERHOME' or 'ACHOME' environment variable set?
==> HINT2: is 'antechamber' in your $PATH?
    What 'which antechamber' in your terminal says?
    'alias' doesn't work for ACPYPE.
ACPYPE FAILED: 1
Total time of execution: less than a second

I am thinking that I have to install amber. But I dont want to do that. Is
there any way that I can create ligand topology for gaff.

On Tue, Aug 1, 2017 at 11:41 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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 Please this GitHub link is totally outdated and not linked in any sense to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
>>>>>
>>>>> * Please search the archive at http://www.gromacs.org/Support
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>>>>>
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>>>>>
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>>>>> send a mail to gmx-users-request at gromacs.org.
>>>>>
>>>>>
>>>>
>>>>
>>>> --
>>>>
>>>>
>>>> *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*
>>>> --
>>>> Gromacs Users mailing list
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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
>
> ==================================================
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
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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*