Re: [AMBER] difference in amino94.xml (MCPB) and all_amino94.lib (leap) for CYM

From: Sangeetha B <sangeetha.bicpu.edu.in>
Date: Wed, 10 Oct 2012 16:57:22 +0530

Jason,

Though both the versions have similar charges for all the other residues,
it is different for CYM.
Thank you for the reply and I will use the leap charges for the backbone
atoms. 

--
Thanks
Sangeetha
On Tue, Oct 9, 2012 at 5:17 PM, Jason Swails <jason.swails.gmail.com> wrote:
> On Tue, Oct 9, 2012 at 12:59 PM, Sangeetha B <sangeetha.bicpu.edu.in>
> wrote:
>
> > Dear Amber users,
> >
> >  I have already posted it a few days back. Since I did not get any
> replies
> > yet and my query lies unsolved, I am reposting this. Sorry for the
> repost.
> >
> > I am using MCPB to generate prep and frcmod files for my protein with
> Zn2+
> > atom coordinated by HieHieCymCym motif.
> > I have successfully generated the prep and frcmod files with restraints
> on
> > all the backbone atoms (CA, H, HA, N, HN, C, O) to the AMBER parm99.dat
> > force field values (ChgModC).
> > When I check the charges generated finally, it is different from the ones
> > seen in $AMBERHOME/dat/leap/lib/all_amino94.lib.
> > When I compare the charges for CYM from
> > $AMBERHOME/dat/leap/lib/all_amino94.lib and
> > file:///usr/local/amber11/dat/mtkpp/amino94.xml, it is completely
> > different.
> >
> >         amino94.xml (MCPB)     all_amino94.lib (leap)
> >
> > N          -0.46300                    -0.415700
> > HN         0.25200                     0.271900
> > CA         0.03500                    -0.035100
> > HA         0.04800                     0.050800
> > CB         0.73600                    -0.241300
> > HB3       0.24400                     0.112200
> > HB2       0.24400                     0.112200
> > SG       -0.73600                    -0.884400
> > C           0.61600                     0.597300
> > O         -0.50400                     -0.567900
> >
> >
> > Why is this difference observed? Someone suggest me which values should
> be
> > used for the CYM backbone atoms (including Hs).
> >
>
> The LEaP versions are 'defined' to be correct.  I would use those.  I don't
> know how or when the MTK++ versions were generated (or if they were even
> supposed to be the same as FF94, although I think they should be).
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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Received on Wed Oct 10 2012 - 04:30:07 PDT
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