Hi Pengfei
It worked for all models.
Thanks
Fabrício
2016-11-01 14:16 GMT-02:00 Pengfei Li <ambermailpengfei.gmail.com>:
> Hi Fabrico,
>
> The problem could be about the wrong total charge during the RESP charge
> fitting.
>
> Which means when MCPB.py calculate the total charge by itself it adds up
> the partial charges in the database and mol2 files you created. This may be
> different from the actual charge of the system.
>
> The quick way to solve this problem is to add “lgmodel_chg" keyword to
> define the large model total charge by yourself and then perform the third
> step modeling of MCPB.py again.
>
> Please let me know whether it works.
>
> Kind regards,
> Pengfei
>
> > On Nov 1, 2016, at 9:58 AM, Fabrício Bracht <fabracht1.gmail.com> wrote:
> >
> > Hi Pengfei. I recently had to redo a parameterization in order to get the
> > original mol2 files. I had to do this because my computer was stolen and
> on
> > the cluster I only had the topology files.
> > Although I used the exact same files, now I get charges that are
> sometimes
> > very different. For example charges of 2.84 on a CT atom and -1.95 on a
> CR
> > atom.
> > I have encountered a similar problem while trying to parameterize a new
> > system which included a ligand. First I thought it was something related
> to
> > the gaussian calculation, but when the same thing happened to the system
> I
> > had already worked on, I figured something might be off.
> > I am using the release2 version of MCPB.py because it seems to be the
> only
> > one that recognizes a N terminal histidine as NHIC (which is one of the
> > residues that binds to the metal atom).
> >
> > Any ideas?
> > Thanks
> > Fabrício
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Received on Tue Nov 01 2016 - 09:30:04 PDT
