Hi, Dan. Thank you so much for your help. This is a great way to try
this. Thanks.
Joyce
On Wed, Oct 31, 2012 at 11:43 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> You could try the 'atommap' command in Cpptraj, which employs a simple
> algorithm to reorder a target structure according to an origin
> structure based on bonding patterns. As long as your ligand is not too
> large (<100 atoms or so) and the # of atoms in target and origin are
> fairly close the algorithm works pretty well.
>
> Say your target is target.pdb and the origin you want it to map to is
> origin.pdb; the command sequence is:
>
> parm target.pdb [target]
> reference target.pdb parm [target]
> parm origin.pdb [origin]
> reference origin.pdb parm [origin]
>
> atommap target.pdb origin.pdb mapout atommap.dat # This creates the atom
> map
>
> trajin target.pdb parm [target]
> trajout reordered.pdb parm [target] # This will print out target.pdb
> reordered according to origin.pdb
>
> Hope this helps, let me know if you try it and run into problems.
>
> -Dan
>
>
> On Wed, Oct 31, 2012 at 2:35 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
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-9119 (Fax)
>
> _______________________________________________
> 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 - 09:30:04 PDT
