[gmx-users] Re:Re: Which FF could be used for protein-RNA MD simulation in GROMACS?

[Thomas Piggot]

Hi Stephan,

The GROMOS DNA and RNA parameters can be found in the 53A6 rtp file. 
This file also has some sugar/carbohydrate parameters (which, however, 
do not seem to accurately match the 45A4 carbohydrate parameters 
published by Lins et al.) and also an entry for DPPC (although there are 
plenty of better united-atom lipid parameters available to download from 
the internet). Whether or not these DNA/RNA parameters should be used 
ahead of AMBER or CHARMM DNA/RNA parameters is another question and I 
would say depends on what is being simulated and why.

Cheers

Tom

lloyd riggs wrote:
> -
>> Message: 1
>> Date: Thu, 9 Dec 2010 23:16:21 -0500
>> From: Vitaly Chaban <vvchaban at gmail.com>
>> Subject: [gmx-users] Re: Which FF could be used for protein-RNA MD
>> 	simulation in GROMACS?
>> To: gmx-users at gromacs.org
>> Message-ID:
>> 	<AANLkTik995O98r7gm8-KLac0xuF9M3rb_43+31Afap7U at mail.gmail.com>
>> Content-Type: text/plain; charset=ISO-8859-1
>>
>> Hey, Shiyong -
>>
>> I believe your problem is related to X2TOP usage rather than to a
>> proper force field choice. I'd suggest to start with looking into N2T
>> files for the below entries.
>>
>> Cheers.
>>
>> --
>> Dr. Vitaly V. Chaban
>> Rochester, U.S.A.
>>
>>
>>>  I just tried G53a6 for protein-RNA simulation. But fatal error shows
>> up.
>>> Opening library file /usr/share/gromacs/top//FF.dat
>>>
>>> Select the Force Field:
>>>  0: GROMOS96 43a1 force field
>>>  1: GROMOS96 43a2 force field (improved alkane dihedrals)
>>>  2: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
>>>  3: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
>>>  4: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
>>>  5: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
>>>  6: [DEPRECATED] Gromacs force field (see manual)
>>>  7: [DEPRECATED] Gromacs force field with hydrogens for NMR
>>>  8: Encad all-atom force field, using scaled-down vacuum charges
>>>  9: Encad all-atom force field, using full solvent charges
>>>
>>> Best
>>>
>>> --
>>> Shiyong Liu
>>
>> ------------------------------
> 
> 
> Dear Shiyong Liu,
> 
> I have run across RNA/DNA .itp/.rtp files by searching (for a while) on the internet, a year or so back, which are/were compatable with the G53a6 FF.  Aside from that though, I don't remember which lab/site had them.  The same is true for lipid and carbohydrate .itp/.rtp libraries.
> 
> Stephan Watkins

-- 
Dr Thomas Piggot
University of Southampton, UK.