Dear Francois,
I attached the leap.log files. I run it twice with the H added to the peptide, here I got error about missing parameters leap1.log, I loaded pep1_H.pdb. I also try to remove hydrogens from the peptide and I loaded the GLYCAM_06 ff here I got strange H conformations on the sugar ring. I checked the atom types and they are identical with the FF libs, the file obtained from RED is MGR.mol2.
/Urszula
________________________________________
Von: FyD [fyd.q4md-forcefieldtools.org]
Gesendet: Montag, 14. Mai 2012 12:40
An: AMBER Mailing List
Betreff: Re: [AMBER] problems with added hydrogens to non standard residue
Urszula,
> I have a peptide with a non standard amino acid, parameters/lib were
> prepared using RED server. After loading this peptide into the
> xleap, program added hydrogens in strange conformations (residue
> name is MGR and the H atoms H4, H2 connected to C3 and H1,H3
> connected to C2. I attached the pdb file. Could someone tell me
> what is wrong here? or how to correct it?
could you send the LEaP script you used?
(this would help to track what is the problem...)
you should load the Amber FF libraries
the FF library(ies) generated by R.E.D. Server
then you load the PDB file (entire peptide)... A match between the FF
libs and the PDB file will occur only if the atom and residue names
are identical in these FF libs and PDB file. If some atoms are missing
in the PDB file, they will be automatically added by LEaP according to
the atoms available in the FF libs...
regards, Francois
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- application/octet-stream attachment: MGR.off
Received on Mon May 14 2012 - 05:00:04 PDT
