Dear Sir,
Thank you very much for working out my problem. However my objective is not
to find out rmsd between IND and the fragments generated, but to rearrange
the trajectory coordinates to the new fragmented format. so that i can use
the fragmented top to read the trajectory for doing mmpbsa decomposition
analysis. I have achieved my objective by writing a code in matlab sir.
Anyway, thanks for your help and support.
Thanks once again,
Rajeswari
On Fri, Aug 1, 2014 at 2:01 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> Sorry it took me so long to get to this.
>
> The two systems (target.top and complex.top) you gave me are laid out
> with the first two molecules forming a protein dimer (residues 1-99
> and 100 to 198); these are identical between complex.top and
> target.top. I assume what you wanted 'atommap' for are the remaining
> components, INX in complex.top (X=1-5) and IND in target.top, where
> INX are smaller fragments of IND.
>
> This really is unfortunately outside the current scope of the simple
> atom-mapping algorithm I came up with. The original intent for
> 'atommap' was for situations where you have the same molecule (perhaps
> from two different programs) that have different atom order, with the
> same of atoms (or at least a very similar number, differing by only a
> few atoms or so). It's not very tolerant of large changes in atoms,
> and trying to map fragments onto pieces ~4x bigger is just asking too
> much.
>
> However, if your only need is to do something like get RMSDs of the
> INX fragments to IND, I notice that the atom names and ordering do
> appear to be the same for the INX fragments and IND, at least for the
> heavy atoms. For example, IN5/IND (0=complex.top, 1=target.top):
>
> > atoms 0 :IN5.N4,C22,C23,O4,C24,C25,C26,C27,C28,C29,C30
> #Atom Name #Res Name #Mol Type Charge Mass GBradius El
> 3201 N4 203 IN5 7 n2 -0.6410 14.0100 1.5500 N
> 3203 C22 203 IN5 7 c3 0.2215 12.0100 1.7000 C
> 3205 C23 203 IN5 7 c3 0.3472 12.0100 1.7000 C
> 3206 O4 203 IN5 7 oh -0.5429 16.0000 1.5000 O
> 3209 C24 203 IN5 7 c3 -0.2684 12.0100 1.7000 C
> 3212 C25 203 IN5 7 ca 0.1310 12.0100 1.7000 C
> 3213 C26 203 IN5 7 ca -0.1432 12.0100 1.7000 C
> 3215 C27 203 IN5 7 ca -0.0313 12.0100 1.7000 C
> 3217 C28 203 IN5 7 ca -0.0801 12.0100 1.7000 C
> 3219 C29 203 IN5 7 ca -0.0756 12.0100 1.7000 C
> 3221 C30 203 IN5 7 ca -0.0244 12.0100 1.7000 C
>
> > atoms 1 :IND.N4,C22,C23,O4,C24,C25,C26,C27,C28,C29,C30
> #Atom Name #Res Name #Mol Type Charge Mass GBradius El
> 3201 N4 199 IND 3 n -0.6410 14.0100 1.5500 N
> 3203 C22 199 IND 3 c3 0.2215 12.0100 1.7000 C
> 3205 C23 199 IND 3 c3 0.3472 12.0100 1.7000 C
> 3206 O4 199 IND 3 oh -0.5429 16.0000 1.5000 O
> 3209 C24 199 IND 3 c3 -0.2684 12.0100 1.7000 C
> 3212 C25 199 IND 3 ca 0.1310 12.0100 1.7000 C
> 3213 C26 199 IND 3 ca -0.1432 12.0100 1.7000 C
> 3215 C27 199 IND 3 ca -0.0313 12.0100 1.7000 C
> 3217 C28 199 IND 3 ca -0.0801 12.0100 1.7000 C
> 3219 C29 199 IND 3 ca -0.0756 12.0100 1.7000 C
> 3221 C30 199 IND 3 ca -0.0244 12.0100 1.7000 C
>
> Since this is the case you can just specify a separate mask for the
> target and reference structures in the rms command, e.g.
>
> parm complex.top
> trajin complex.pdb
> parm target.top
> reference target.pdb parm target.top
> rms reference \
> :IN5.N4,C22,C23,O4,C24,C25,C26,C27,C28,C29,C30 \
> :IND.N4,C22,C23,O4,C24,C25,C26,C27,C28,C29,C30 \
> out IN5_to_IND.dat
>
> Of course, I would check that the naming/ordering is the same for all
> fragments (I checked only IN5 and IN1, which worked).
>
> Hope this helps,
>
> -Dan
>
> PS - Mapping fragments to larger pieces is a *very* interesting and
> potentially useful functionality, so I may look into implementing
> something like that for the next release. Thanks for bringing it to my
> attention!
>
> On Wed, Jul 16, 2014 at 8:04 AM, Rajeswari A.
> <rajeswari.biotech.gmail.com> wrote:
> > Dear amber users,
> > I have two topology files (top1 and top2) in which the structure, charge,
> > coordinates, total atom number everything identical but the atom order is
> > different. I have trajectory that corresponds to topology1. Now i want to
> > reorder the trajectory based on the atom order of top2. I am using
> atommap
> > command of cpptraj in amber14.
> >
> > To test the reordering i tried atommap for single pdb structure using the
> > following command.
> >
> > parm target.top
> > reference target.pdb
> > parm complex.top
> > reference complex.pdb parmindex 1
> > atommap target.pdb complex.pdb mapout atommap.dat
> > trajin target.pdb
> > trajout reordered.pdb pdb
> >
> > I expect target.pdb to reorder similar to complex.pdb. However, the
> > resultant reordered.pdb is not matching with the complex.pdb. Could
> someone
> > help me to sort out this? Detailed log file is attached for your
> reference.
> >
> > Thanks in advance,
> > Rajeswari A.
> >
> > _______________________________________________
> > 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) 585-6208 (Fax)
>
> _______________________________________________
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>
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Received on Fri Aug 01 2014 - 22:30:02 PDT
