On Fri, Apr 20, 2012 at 3:49 PM, DoYong Kim
<doyong.kim.mail.chem.tamu.edu>wrote:
> I have used leaprc.ff99SB
>
I don't understand what you've done. First, leaprc.ff99SB should define
the OXT atom type, so I don't understand why you are getting this error in
the first place. Second, the leaprc files we release alias chain-ending
amino acids with their N- or C-terminal forms, so by default, any PDB that
has an amino acid at either terminus will automatically be converted into
the appropriate, corresponding N- or C-terminal residue. If you need to,
you can disable this behavior by loading a modified leaprc.ff99SB instead
(just take out the section that aliases the termini).
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
> ion)
>
> then when I save the parameters, prmtop and inpcrd files, I get errors
> saying,
> 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.
>
I think we would need your full set of commands. Based on the information
provided, this error should not have occurred, unless I missed something.
HTH,
Jason
>
> 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 <case.biomaps.rutgers.edu> 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)
> >>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.)
> >
> > ...dac
> >
> >
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>
> Kim, Doyong
> Department of Chemistry
> Texas A&M University
>
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Sat Apr 21 2012 - 07:30:06 PDT
