Thanks for the reply. You were right, the charges were lost at the tleap
stage because I saved the system to a pdb file and reloaded it. I had the
impression that tleap saves in memory the properties (including the
charges) of the ligand, so when I reloaded it, it would recognize it from
the residue name and assign the appropriate charges. Unfortunately, this is
not the case, as a result, the "complex.prmtop" file had charge 0.0 for all
ligand atoms.
Regardless of the charges, I have noticed some differences in the atom
types (carboxyl) before and after writing the mol2 from the trajectory, as
well as some valence issues. I will double check that I am not doing
something wrong and perhaps come back later with details.
best
Thomas
On 22 November 2017 at 18:44, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> What version of cpptraj are you using? Also, what are you using as
> your input topology? Does it have charges?
>
> -Dan
>
> On Wed, Nov 22, 2017 at 11:04 AM, Thomas Evangelidis <tevang3.gmail.com>
> wrote:
> > Hi,
> >
> > This question refers to Daniel Roe. I am doing some post-processing of
> > ligand trajectories and I need to have all the frames into a .mol2 file.
> I
> > currently write such a file from the trajectory like this:
> >
> > trajin complex.prod_GB.nc 50 100 1
> > strip !:LIG
> > trajout multiframe_lig.mol2 sybyltype
> > go
> > quit
> >
> > Is it possible cpptraj to write out the partial charges to the last
> column
> > of the mol2 file? Currently, it writes 0.0 to all atoms. If not, could it
> > be programmed easily and hopefully have it as a patch for AmberTools?
> >
> > Thanks,
> > Thomas
> >
> >
> > --
> >
> > ======================================================================
> >
> > Dr Thomas Evangelidis
> >
> > Post-doctoral Researcher
> > CEITEC - Central European Institute of Technology
> > Masaryk University
> > Kamenice 5/A35/2S049,
> > 62500 Brno, Czech Republic
> >
> > email: tevang.pharm.uoa.gr
> >
> > tevang3.gmail.com
> >
> >
> > website: https://sites.google.com/site/thomasevangelidishomepage/
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe
> Laboratory of Computational Biology
> National Institutes of Health, NHLBI
> 5635 Fishers Ln, Rm T900
> Rockville MD, 20852
> https://www.lobos.nih.gov/lcb
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
======================================================================
Dr Thomas Evangelidis
Post-doctoral Researcher
CEITEC - Central European Institute of Technology
Masaryk University
Kamenice 5/A35/2S049,
62500 Brno, Czech Republic
email: tevang.pharm.uoa.gr
tevang3.gmail.com
website: https://sites.google.com/site/thomasevangelidishomepage/
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Received on Wed Nov 22 2017 - 17:30:03 PST
