Thank you Francois,
I developed a lib for a terminal Lysine residue, LYA.mol2. However after loading everything together with the peptide.pdb I have still errors regarding the parameters,
I attached the files:
LYA.mol2 - terminal Lysine
MGR.mol2 - sugar-res
pep1_H.pdb - peptide
leap.log
What parameters are missing now? its not very clear from leap.log ...
Thank you in advance for your help
/Urszula
________________________________________
Von: FyD [fyd.q4md-forcefieldtools.org]
Gesendet: Dienstag, 15. Mai 2012 09:07
An: AMBER Mailing List
Betreff: Re: [AMBER] problems with added hydrogens to non standard residue
Urszula,
> 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.
Many problems...
See
http://q4md-forcefieldtools.org/Help/Urszula/
First, I modified the atom names in 'pep1_H.pdb' so that they match
these in the Amber FF libs.
Then, I created a 'leap.cmd' file; pay attention here to the GLYCAM
version you wish to use; if you use the last version of GLYCAM you
might have to modify the atom types in MGR...
You have a terminal Lysine with an aldehyde function; if this terminal
amino-acid is indeed a 'Lysine-aldehyde' you should develop a new FF
lib for this residue as well.
See
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#18
then, once all that will be corrected you will be able to create a new
leap.cmd script...
regards, Francois
> ________________________________________
> 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
Received on Tue May 15 2012 - 05:00:04 PDT
