[gmx-users] OPLS-AA atom types

Justin A. Lemkul jalemkul at vt.edu
Tue Apr 5 18:45:36 CEST 2011

Mark Abraham wrote:
> On 6/04/2011 1:28 AM, Mark Abraham wrote:
>> On 6/04/2011 1:00 AM, Austin B. Yongye wrote:
>>> Thanks Justin.
>>> It still doesn't solve my problem, e.g., there are several instances 
>>> of CT with diferent opls_??? numbers, but no indication of their 
>>> environments; they could represent C bonded to 1->4 carbon atoms, 
>>> etc. There's no way of telling. I contacted one of the opls folks 
>>> last week, but got no response. So I thought I could enlist the help 
>>> of gromacs users.
>> Yes, but you're making it hard to help you by forcing us to guess what 
>> content you're looking at. Our time is valuable, and you're not making 
>> it easy for us to give the minimum amount :-) Tell us what file you 
>> looked at, what you saw (copy and paste), and why it's not useful.
> Ah, I see the problem. Justin recommended the wrong file, and you didn't 
> guess the right one from the filenames. You should look at 
> atomtypes.atp, and literature references therein.

Based on the original question (mapping between names and numbers), I thought I 
had provided the requested information.  If I've ended up wasting anyone's time, 
I apologize.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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