Thanks Daniel & David,
Ok, i'll redo the system preparation considering unique atom names per small molecule. However tleap didn't warn me about anything and didn't crash or resulted in an error either. This is why I stupidly assumed that things are working great. The simulation runs also fine (with the full ligand, no atoms missing).
Is this due to the fact that I load a mol2 file into tleap and later combine with a PDB, rather than putting the ligand into the PDB file?
Thanks again for the very quick help !
Peter
-----Message d'origine-----
De : David A Case [mailto:david.case.rutgers.edu]
Envoyé : mardi 19 avril 2016 20:20
À : AMBER Mailing List
Objet : Re: [AMBER] atom serials instead of residue names and atom names in nativecontacts cpptraj
On Tue, Apr 19, 2016, peter.schmidtke.discngine.servier.com wrote:
>
> In natural residues yes. But sometimes I have small molecules where
> the atom name is not unique (as output of tleap). Like for instance
> for ATP. This is actually the problem.
This is illegal, and tleap should be warning you about this. It will use the first atom of a given name, and ignore the rest (which accommodates "alternate conformers" that are often present in PDB files.) It's not clear how you created the ATP libraries (and I don't need to know this), but you should avoid this situation--as Dan pointed out, all kinds of programs, including cpptraj, assume that atom names are unique within residues.
...regards...dac
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Received on Wed Apr 20 2016 - 01:30:06 PDT
