[gmx-users] gromacs charges

Valentin Gogonea v.gogonea at csuohio.edu
Mon Sep 30 18:36:59 CEST 2002

Hi Erik,

If charges for all OPLS atom types are specified in ffoplsaanb.itp, 
does the reading format for  ffoplsaa.rtp require to specify the 
charges in the topology of the molecule. I mean do I have still to fill 
in the charges in the rtp file? I saw that in ffoplsaa.rtp the charges 
for all amino acids are specified even they are given in ffoplsaanb.itp.

If I need to introduce a new OPLS atom type (e.g. sulfonium ion 
[SR3]+), what code should I give to it? Codes run up to opls_965 in 
foplsaa.atp file.


On Friday, September 27, 2002, at 01:00 PM, Erik Lindahl wrote:

> quantix1 at gmx.de wrote:
>> Dear Gromacs-Users,
>> I am completely new to Gromacs. Let's say, I'm still thinking about 
>> using
>> it. My first question is, how charges for non-standard amino acids or 
>> other
>> molecules are usually derived for the force field in Gromacs. Is 
>> there a
>> procedure which is considered to be standard and gives the most 
>> consistent results (like the HF/6-31G -> RESP for AMBER) ?
>> This should be enough before the weekend. Thanks in advance,
>> Uwe
> When it comes to building new molecules, nothing beats the Jorgense 
> OPLS-AA/L forcefield (yes, it's available in Gromacs even if the 
> webpages don't mention it). The nice thing about OPLS is that all 
> groups
> are designed and parameterized as "building blocks", so you can attach 
> a
> new functional group to e.g. a protein, and you will only have to 
> update
> the charge of one or two atoms. Check the file share/top/ffoplsaa.atp 
> for comments on all the different atom types.
> OPLS charges are derived with CHELPG, and for proteins all the backbone
> dihedrals have been parameterized not only to reproduce the position of
> the minima, but the actual form of the energy landscape.
> The AMBER forcefield is on our todo-list, but we've never felt really 
> motivated since OPLS/AA is better in most cases.
> Cheers,
> Erik
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