[gmx-users] RE: Regarding errors

[Dallas Warren]

First suggestion is check the existing resources that already exist to help you with problems with GROMACS.  Start with the error page on the website http://www.gromacs.org/Documentation/Errors it has further details on more common the errors that you may encounter.

Second suggestion is to check out the support page http://www.gromacs.org/Support which has some great advice on what to do, including general etiquette in asking for help.  I have replied to your email to the emailing list, which is where discussions like this should be held, unless you are paying me for support ;-)  If you followed the advice there your searching would have pulled up some very similar questions from other users on the emailing list, with a number of possible reasons and solutions.  Plus you would have found the link below I have provided.  You should always check the existing resources first, since for those starting out it is highly unlikely to encounter something that hasn't been seen, discussed and solved before.  If you do that, it will be far faster than waiting for some unknown person to provide you an answer, and you will learn more in the process.

For the particular error you have observed see http://www.gromacs.org/Documentation/Errors#Atom_X_in_residue_YYY_not_found_in_rtp_entry

If that is not the reason, there are a couple of others that I have noticed being mentioned on the emailing list.

Catch ya,

Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at monash.edu
+61 3 9903 9304
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail.

From: seera suryanarayana [mailto:palusoori at gmail.com]
Sent: Tuesday, 1 May 2012 7:25 PM
To: Dallas Warren
Subject: Regarding errors

Hello,
       While i am running the gromacs software i am getting the following error.
Fatal error:
Atom HA in residue MET 1 was not found in rtp entry MET with 11 atoms
while sorting atoms.
Is there any explanation why is this happening?
I eould appreciate any help.
I am new in using MD and gromacs in particular.

Thanks and regards
Suryanarayana Seera,
Juniur Research Fellow,
India.
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