[gmx-users] Re: fatal error......

[K.A.Feenstra]

seema namboori wrote:
> 
> Hello,
> I am student of IIT,Bombay.
> I am using Gromacs 2.0.
> I ran the pdb2gmx program.but it does not give any
> output.It shows a fatal error saying the:
> 
> Fatal error: Chain identifier 'D' was used in two
> non-sequential blocks (residue 7, atom 194)
> 
> My pdb file is that of nucleotides.
> 
> please let me know as to what is the problem.why am i
> getting such an error message.

Dear Seema,

These quiestions should preferably be directed to the gromacs
users mailinglist (gmx-users). That improves you chances of a quick
response since it allows many more people to read your questions.
You can only post to the list if you are subscribed, if you are not
I suggest you subscribe from the web-site www.gromacs.org.
For now, I'll also cc this mail to the list.

To answer your question: pdb2gmx uses chain identifiers to identify
separate chains (could be protein or dna). If you use a certain
identifier (let's say 'D') for a certain chain, but later on in your
pdb file it is used for another chain, pdb2gmx simply refuses to
sort that out. It cannot know wether you want the two chains to be
separate or combined. So you should either put both parts next to
each other in the file if they should be one, or give them separate
identifiers if they should be separate chains (or molecules).

-- 
Groetjes,

Anton
 _____________ _____________________________________________________
|             | Anton Feenstra       Dept. of Biophysical Chemistry |
|  _   _  ___,| K.A.Feenstra at chem.rug.nl    University of Groningen |
| / \ / \'| | | Tel +31 50 363 4327                    Nijenborgh 4 |
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| \_/ \_/ | | | http://md.chem.rug.nl/~anton        The Netherlands |
|             | "Why, how now, Claudio ! Whence Comes this Restraint|
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