[gmx-users] Re: Error while doing EM in DMSO.
David van der Spoel
spoel at xray.bmc.uu.se
Thu May 17 12:33:56 CEST 2007
Anil Kumar wrote:
> Dear David,
> Thanks for advice, i had made the changes but still getting the same error
> 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.
> With Regards
>> 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
>> If the problem is the missing masses, then just add them in the [atoms]
>> section. (Chapter 5)
they should be added in the top file. the atp is not used for anything
(except for confusing people unfortunately)
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
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