AMBER Archive (2007)

Subject: Re: AMBER: xleap question

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Fri Sep 14 2007 - 11:32:20 CDT

you could turn off residue name mapping using clearpdbresmap in leap.
that will leave the residues as normal rather than N/C terminal.

On 9/14/07, Anna Díaz Cirac <anna.dcirac_at_gmail.com> wrote:
>
> Dear Amber users,
>
> i use xleap to create a cyclic peptide, and i use head and tail amino
> acids to constructed it and with bond command i connect both extrems to get
> the cyclic peptide. Then i minimizate the structure and get a good
> structure. Using AMBPDB i get the pdb file, and finally take the pdb to
> xleap again to obtain de structure solvated. But the problem is that, when i
> load the pdb i have an error:
>
> Added missing heavy atom : .R<CGLN 10> .A<OXT 18>
> total atoms in file: 199
> leap added 1 missing atom according to residue templates
>
> Leap change my GLN to CGLN and put a OXT atom in the terminal Cterminal. I
> tried to seleted it again, erase it, bond again and sovated it....but of
> corse i had problems with the unperturbed charge.
>
> There's any reason why this happends? What I'm doing is the best way to
> obtain the cyclic? Others visual programs understand the connection of
> extrem amino acid.
>
> And why if i use desc name.residue.atom doesn't say double bond in C=0 of
> amino acid? or the program knows the distance?
>
> Thanks and best regards
>
> --
> Adéu
> Anna

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