Re: [AMBER] dna

From: <>
Date: Fri, 25 Jun 2010 13:24:33 +0530 (IST)

> On Wed, Jun 23, 2010, wrote:
>> > The easiset and best thing to do is to upgrade to the current version of
>> > AmberTools (which contains nab).
>> nab version is updated and no problem during pdb generation.
> Can you say exactly what you mean by "nab version is updated"? What did you do?
> When I run your "" file, I get a different pdb file. The first atom
> of my file is named "HO5'", not "H5T'". (Maybe you are accidentally running
> an earlier version of nab. Check you PATH and AMBERHOME variables.)
> Also, you can learn a lot by studying carefully what the log file reports.
> ....dac
> _______________________________________________
> AMBER mailing list
very sorry
actually i also got HO5' only but seeing some tutorial referance i changed to
H5T. so i'm running amber9 +tools 1.2
and did u see that the terminal residues are not correctly bonded.
still i am facing same problem of not getting parameters
can u help wat should i learn here from the logfile.
i just want to generate the topology and coordinate file for this dna.
i don't understand why error is coming of atom mismatch.

waiting for the help

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Received on Fri Jun 25 2010 - 01:00:05 PDT
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