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 16:44:40 +0530

Ben,

Thanks for your kind reply. To be clear of what I did, I used CYM as a
template to create a new residue in MCPB and generated charges for the
whole cluster, i.e Zn2+ along with the residues HHCC. In this process I
have restrained the charges of the backbone atoms to be equivalent to
parm99 and the charges on the side chain atoms were allowed to change
according to the presence of Zn2+.

Is this the correct way to proceed? Any suggestions in this regard would be
very helpful.

Thanks in advance.

--
B. Sangeetha
On Wed, Oct 10, 2012 at 1:44 AM, Ben Roberts <ben.roberts.geek.nz> wrote:
> For clarity, the MCPB charges are obtained by RESP fitting to the metal
> cluster as a whole, in a geometrically unoptimised conformation.
>
> This means that if you're using MCPB charges for part of the cluster, it
> may be better to use them for the whole cluster (including the side chains).
>
> If you just wanted to use a CYM residue by itself, I'd use the LEaP
> charges.
>
> Cheers,
> Ben
>
> On 10/10/2012, at 12:47 AM, Jason Swails 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> --
> For greater security, I support S/MIME encryption.
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber

Received on Wed Oct 10 2012 - 04:30:05 PDT