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

[Kamalesh Roy]

whenever I am running the pd2gmx it is giving me an error
"OLA not found in residue topology database"


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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