Hi, Thomas. Thank you so much for your help.
I will try xleap to see if it works for pairs with larger transformation.
Thanks for this suggestion.
Best regards,
Joyce Huang
On Wed, Oct 31, 2012 at 4:35 AM, <steinbrt.rci.rutgers.edu> wrote:
> Hi Joyce,
>
> in case the ligand files come from some third party software that does
> completely mix up the atom order (e.g. because an additional group changes
> the numbering order in a ring), there is probably really no way around
> rebuilding them by hand.
>
> When ligands are fairly similar it may help to draw their common core in
> xleap, save that fragment and then build each ligand from the fragment and
> saving it as mol2. I think the common atom order will be the same in that
> case.
>
> Take care, when you run such a ligand through antechamber, e.g. for
> charges, it may reorder the atoms again. Some hand manipulation/checking
> is certainly involved in this, I think there is no reliable automated way
> yet. This may change in Amber13, though...
>
> Kind Regards,
>
> Thomas
>
> On Tue, October 30, 2012 4:48 pm, Jodi Ann Hadden wrote:
> > Hi Joyce,
> >
> > This seems like an unnecessary complication.
> >
> > Since you are doing TI in AMBER11, I assume you are using soft core
> > potentials instead of the dummy atom method, and you have separate
> > topology files that represent the lambda=0 and lambda=1 end states. In
> > this case, you only have to make sure the common atoms from each state
> are
> > in the same order in the two separate files, that is, the atoms that are
> > not going in your scmask. If the common atoms are in the same relative
> > order, but just have scmask atoms in between them, that is fine.
> > Everything else just has to be the same ignoring scmask atoms. Since your
> > scmask is only one or to atoms, this should be pretty easy to ensure
> > without excessive file manipulation. You don't have to move the ligand
> > differences to the end of the file as long as you are specifying them in
> > your scmask.
> >
> > Hope this helps,
> > Jodi
> >
> > Jodi Hadden
> > GLYCAM Lab
> > Complex Carbohydrate Research Center
> > University of Georgia
> >
> >
> > On Oct 29, 2012, at 10:35 AM, Yulin Huang
> > <yulinhuang2007.gmail.com<mailto:yulinhuang2007.gmail.com>> wrote:
> >
> > Dear Amber users:
> > I am performing binding free energy calculation for a kinase with
> > 12 ligands using thermodynamic integration (AMBER11). It seems that the
> > atom names and orders for the corresponding atoms in these 12 ligands in
> > the initial setup have to be the same. Thus the
> > parm files and crd files generated after I use the antechamber, parmchk
> > could be the same
> > for the corresponding atoms. After that, the small mask (one or two
> > atoms)
> > can be specified for calculations.
> >
> > I have manually made all the corresponding atom names the same. Now I am
> > trying to make the order the same. It is not an easy task. The way I do
> > is
> > to put all the different atoms among 12 ligands at the end of ligand mol2
> > files. But I have to change all the connectivity part. I've tried to
> > load
> > the mol2 file into software MOE and output the pdb file and then convert
> > to
> > mol2 file. But the different atom such as O will be placed in the middle
> > of the mol2 file automatically. But I have to put the different atoms
> in
> > the end to make the corresponding atoms in the same order.
> >
> > Does anyone has any ideas for this problems? Many thanks in advance.
> >
> > --
> > Yulin "Joyce" Huang
> > Ph.D Candidate
> > Computational Chemistry (CADD)
> > Advisor: Dr. Robert C. Rizzo
> > State University of New York at Stony Brook
> > Stony Brook NY,11790
> > Office: (631)632-8519
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org<mailto:AMBER.ambermd.org>
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> Dr. Thomas Steinbrecher
> formerly at the
> BioMaps Institute
> Rutgers University
> 610 Taylor Rd.
> Piscataway, NJ 08854
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Yulin "Joyce" Huang
Ph.D Candidate
Computational Chemistry (CADD)
Advisor: Dr. Robert C. Rizzo
State University of New York at Stony Brook
Stony Brook NY,11790
Office: (631)632-8519
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Oct 31 2012 - 09:00:02 PDT
