Urszula,
If you are sure that atom types and order of atoms are indentical:
- are you sure that you have used the same molecule in RED and in leap?
Do you have some chiral centers on your sugar?
This type of warnings in your log file could arise from RED parameters
developped for R enantiomer and used in leap for S enantiomer (or
inverse).
Renata
> 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
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
*****
Université de Nantes
CEISAM UMR 6230
2 rue de la Houssiniere
44322 NANTES Cedex 3
France
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon May 14 2012 - 05:30:03 PDT
