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

[David van der Spoel]

Anil Kumar wrote:
> 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)
>>
>> --
they should be added in the top file. the atp is not used for anything 
(except for confusing people unfortunately)

-- 
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
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