I confirm that the mol2 does NOT come from antechamber. Fixed the unique numbering on my side already. Then for Daniel, the request to output atom serials isn't really necessary.
Cheers.
Peter
-----Message d'origine-----
De : David A Case [mailto:david.case.rutgers.edu]
Envoyé : mercredi 20 avril 2016 14:10
À : AMBER Mailing List
Objet : Re: [AMBER] atom serials instead of residue names and atom names in nativecontacts cpptraj
On Wed, Apr 20, 2016, peter.schmidtke.discngine.servier.com wrote:
>
> 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?
That could be the problem, in which case it arguably is a bug in the
loadMol2() routines. We are probably assuming the mol2 files (which usually come from antechamber, which in turn enforces unique atom names) obey this rule, but that might not be true. I'll enter this as a bug.
...thanks...dac
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Received on Wed Apr 20 2016 - 06:00:06 PDT
