[gmx-users] gromacs.org_gmx-users Digest, Vol 135, Issue 5

Timofey Tyugashev tyugashev at niboch.nsc.ru
Thu Jul 2 06:35:40 CEST 2015

No, I may have misleadingly phrased my question but I do use 8-oxoguanosine parameters calculated and published in a paper for AMBER years ago. I am simply worried about correctly formatting them into force field definition files in GROMACS.
A far simpler task than calculating and verifying the numbers themselves all by myself.

01.07.2015 18:51, gromacs.org_gmx-users-request at maillist.sys.kth.se пишет:
> ------------------------------ Message: 6 Date: Wed, 01 Jul 2015 
> 08:41:09 -0400 From: Justin Lemkul <jalemkul at vt.edu> To: 
> gmx-users at gromacs.org Subject: Re: [gmx-users] Protein-DNA simulation 
> LINKS error Message-ID: <5593DFE5.20806 at vt.edu> Content-Type: 
> text/plain; charset=windows-1252; format=flowed On 7/1/15 8:08 AM, 
> Timofey Tyugashev wrote:
>> >Thanks for the advice, Justin and Mark.
>> >
>> >After rerunning the simulation with guanine in the DNA I've found no noticeable
>> >problems.
>> >Now I'm looking for another possible sources for mistakes.
>> >1.The input PDB file is formatted using amber conventions, i.e. DG5 and DG3 for
>> >terminal guanosine  residues, CYX for S--S linked cystine and so on. Could it
>> >result in any erroneous interpretations by pdb2gmx?
> pdb2gmx throws obvious errors if there is a problem.  AMBER uses unique
> nomenclature for termini, which is consistent with what you describe here.
>> >2. I think I correctly created 8-oxoguanine entry in amber force field files by
>> >copying and modifying existing one for normal guanine, but I want to re-check
>> >myself just to be sure. Is there anything more in-depth available than rather
>> >laconic instruction from the GROMACS site? I've tried searching through the
>> >maillist, but looks like nothing similar came up (It's a pity that no forum
>> >exist, looking for past answers would be far simpler).
> Generating force field parameters is well beyond the scope of what is or should
> be included in GROMACS documentation.  We provide a few resources in terms of
> the implementation, but given the vast scope of this topic, and the expert
> knowledge required, it is impossible to teach people to derive parameters
> suitably.  For that, you need to read and understand the literature regarding
> the parametrization theory and methods of your chosen force field.  At least
> you've arrived at your answer - you have sub-optimal parameters for 8-oxoG that
> cause a crash.  Now the task is to derive parameters of suitable quality.

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