[gmx-users] Re: Error while doing EM in DMSO.

[Anil Kumar]

Dear David,

Thanks for advice, i had made the changes but still getting the same error
that

Fatal error:
Atomtype 'SD' not found!

SDMSO  32.06000 ;     DMSO Sulphur (solvent)
CDMSO  15.03500 ;     DMSO Carbon (solvent)
ODMSO  15.99940 ;     DMSO Oxygen (solvent)

**************Changes Made in ffG43a1.atp file***********************
SD  32.06000 ;     DMSO Sulphur (solvent)
CD  15.03500 ;     DMSO Carbon (solvent)
OD  15.99940 ;     DMSO Oxygen (solvent)

I am totally helpless and clueless in finding my mistakes.Any help,hint,
suggestions are most welcome.

Thanks,
With Regards
anil

>
> Today's Topics:
>
>    1. Re: Error while doing EM in DMSO. (David van der Spoel)
> Date: Wed, 16 May 2007 21:07:54 +0200
> From: David van der Spoel <spoel at xray.bmc.uu.se>
> Subject: Re: [gmx-users] Error while doing EM in DMSO.
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <464B568A.9080705 at xray.bmc.uu.se>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Anil Kumar wrote:
>> Dear Users,
>>
>> First of all thank you Mark, yes you are right. it was problem of force
>> field and topoloy file mismatch.
>> I have made changes in the ffG43a1 residue toplogy file for DMSO., but
>> still getting the same error. Please let me know if i am doing some
>> mistake.
>>
> If the problem is the missing masses, then just add them in the [atoms]
> section. (Chapter 5)
>
> --
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,  	75124 Uppsala, Sweden
> phone:	46 18 471 4205		fax: 46 18 511 755
> spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
> +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++