Re: [AMBER] about sybylmol2 file

From: case <>
Date: Fri, 11 Jun 2010 09:19:52 -0400

On Fri, Jun 11, 2010, Navanath Kumbhar wrote:
> I want to do simulation of modified nuclesodies with anticodonloop
> structures by using sybyl mol2 file as input file format. I opened this file
> in xleap by using gaff force field but when i go to save it it gives
> for atom: .R<UNK0001 1 >. A < H108 285 > could not find type : H

See tutorial B4 for instructions on building libraries for molecules not in
the standard database. You can't just open an arbitrary mol2 file in xleap --
running antechamber is generally needed.

You should also check the link on the Amber web site for "modified nucleosides
for RNA". This site has lots of anticodonloop nucleosides; even if it doesn't
have exactly the one you need, it may get you close.


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Received on Fri Jun 11 2010 - 06:30:15 PDT
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