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.
>
> _______________________________________________
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> 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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Received on Thu Jul 31 2014 - 14:00:02 PDT
