[gmx-users] AMBER LIPID14 ff in GROMACS

[Christopher Neale]

Possibly build in amber and then convert to gromacs input format with parmed: https://github.com/ParmEd/ParmEd/issues/631


Looks like it might be a little tricky and of course you'd want to compare single-point energied in amber and then in the gromacs port, though that is complicated by code differences (e.g. as described in https://link.springer.com/article/10.1007/s10822-016-9977-1 )<https://link.springer.com/article/10.1007/s10822-016-9977-1>


Not sure if Intermol would make that conversion task easier or harder, but it's here: https://github.com/shirtsgroup/InterMol



________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Amit Singh <doctorandi at gmail.com>
Sent: 01 June 2017 12:50:14
To: Mark Abraham
Cc: gmx-users at gromacs.org; gromacs.org_gmx-users at maillist.sys.kth.se; sudip.cupb at gmail.com
Subject: Re: [gmx-users] AMBER LIPID14 ff in GROMACS

Hello Mark,
     Thank you very much for your prompt reply. Recently, Pluhackova K. *et
al have *reported a work
*(Ref: "A Critical Comparison of Biomembrane Force Fields: Structure and
Dynamics of Model DMPC, POPC, and POPE Bilayers" **DOI*

*: 10.1021/acs.jpcb.6b01870) related to the use of Amber Lipid14 force
field for Gromacs. Importantly, In their work, they have given a link for
*.itp file, which is not working now a days. In this regard, I am looking
your assistance.*
*Have a nice day,*

On Thu, Jun 1, 2017 at 7:05 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> I'm not aware of anybody who's done this. It's a lot of work to produce
> both the conversion and run a verification suite, which as far as I know
> the AMBER forcefield developers don't make available even for AMBER
> simulation package users.
>
> Mark
>
> On Wed, May 31, 2017 at 6:49 PM Amit Singh <doctorandi at gmail.com> wrote:
>
>> Is there any way to use Amber Lipid14 force field parameters for GROMACS
>> --
>> सस्नेह / with regards
>> अमित सिंह / Amit Singh
>> कम्प्यूटेशनल विज्ञान केंद्र / Centre for Computational Sciences
>> बुनियादी और अनुप्रयुक्त विज्ञान स्कूल / School of Basic and Applied
>> Sciences
>> पंजाब केन्द्रीय विश्वविद्यालय / Central University of Punjab
>> बठिंडा / Bathinda 151 001
>> भारत / INDIA
>> --
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--
सस्नेह / with regards
अमित सिंह / Amit Singh
कम्प्यूटेशनल विज्ञान केंद्र / Centre for Computational Sciences
बुनियादी और अनुप्रयुक्त विज्ञान स्कूल / School of Basic and Applied Sciences
पंजाब केन्द्रीय विश्वविद्यालय / Central University of Punjab
बठिंडा / Bathinda 151 001
भारत / INDIA
--
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