Re: [AMBER] xleap pdb file loading problem.

From: DoYong Kim <>
Date: Fri, 20 Apr 2012 14:49:59 -0500

I have used leaprc.ff99SB

when I load the pdb extracted from my SA results, xleap adds oxygen as OXT
on c-terminus glycine. (my peptide is RVGVAPG+ Na ion resulting 1+ charge

then when I save the parameters, prmtop and inpcrd files, I get errors
warning the unperturbed charge of the unit: 2.00100 is not zero
FATAL : Atom .R<GLY 7>.A<OXT 8> does not have a type.
failed to gerenate parameters
parameter file was not saved.

the problem I see is that I have 2 as charge instead of 1 and the atom added
by the xleap does not have a type.

Thank you in advanced,
Doyong kim

On Thu, 19 Apr 2012 14:47:55 -0400
  David A Case <> wrote:
> 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)
>> xleap recognise the c-terminus gly as just GLY and adds oxygen to
>> 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
>> 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
> leaprc file. (It may also be that leap for some reason is not
> 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.)
> ...dac
> _______________________________________________
> AMBER mailing list

Kim, Doyong
Department of Chemistry
Texas A&M University

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Received on Fri Apr 20 2012 - 13:00:03 PDT
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