Re: [AMBER] xleap pdb file loading problem.

From: David A Case <>
Date: Thu, 19 Apr 2012 14:47:55 -0400

On Thu, Apr 19, 2012, DoYong Kim wrote:
> I started my initial structure by xleap and made my structres and used CGLY
> for my c-terminus gly. Then after SA i used ptraj to extract structre in to
> pdbs. then now I load those pdb files(qwe= loadpdb *.pdb command) and
> xleap recognise the c-terminus gly as just GLY and adds oxygen to the
> strucutre. This leads me in to error when I try to save ( atom does not have
> type). In this case what should I do to pdb files or how to load pdb files
> in to xleap.

We need more details, in particular which leaprc file you used. The
translation of the C-terminal glycine from GLY to CGLY is defined in the
leaprc file. (It may also be that leap for some reason is not recognizing
your GLY as being at the C-terminus: look carefully at what xleap prints out
after the loadpdb command, since that gives a lot of information about exactly
what is going on. If it doesn't recognize the end of your chain, you will be
able to see that.)


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Received on Thu Apr 19 2012 - 12:00:02 PDT
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