[gmx-users] Oleic acid.....topology problem...

[Justin Lemkul]

On 3/29/15 10:42 PM, Kamalesh Roy wrote:
> whenever I am running the pd2gmx it is giving me an error
> "OLA not found in residue topology database"
>

You don't need pdb2gmx.  The purpose of pdb2gmx is to generate a topology.  The 
purpose of PRODRG is to generate a topology (albeit, as I said, likely a 
suboptimal one).  So if you ran PRODRG you already have a topology and do not 
need to process oleic acid via pdb2gmx.

See, for instance, 
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html

-Justin

>
> On Sun, Mar 29, 2015 at 10:59 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 3/28/15 11:33 PM, Kamalesh Roy wrote:
>>
>>> Dear all,
>>>
>>> I am using gromacs latest version in Ubuntu...
>>> I am trying to simulate oleic acid in a box with some protein.
>>> Have made the .itp from prodrg server... incorporate the same still not
>>> recognizing OLA residue.
>>>
>>>
>> PRODRG parameters always require manual refinement, and the old(er)
>> version of the GROMOS force field that it supports will probably have an
>> inadequate description of the alkyl chains.  Look into newer parameters,
>> e.g. those derived from 53A6.
>>
>>   I have change the aminoacid.rtp also....
>>>
>>>
>> You shouldn't.
>>
>>   Can anybody suggest me the procedure ......
>>>
>>>
>> You haven't really said what you've done, so it's pointless to guess where
>> the problem is.  You haven't even said if there's a specific error that
>> you're getting.  If you want free and efficient help, you need to make it
>> easy to provide it.
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 629
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================