Re: [AMBER] Problem with atommap in cpptraj

From: Daniel Roe <>
Date: Wed, 16 Jul 2014 22:47:52 -0600


Unfortunately this system (3000+ atoms) is larger than anything I have ever
tested atommap on (~100 atoms), so you may just be hitting the limits of
the simplistic algorithm I used for matching (as evidenced by the multiple
"Warning: mapByIndex: Atom XXXX in reference is unique but not mapped!"

If you can send me off-list your target/complex PDBs I may be able to help
more, but my feeling is that poor atommap may just be overwhelmed. Also, if
you can provide any more details about your problem, such as how the atom
ordering came to be different, I (or others) may be able to offer
alternative suggestions.



On Wed, Jul 16, 2014 at 8:04 AM, Rajeswari A. <>

> 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
> reference target.pdb
> parm
> 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

Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Wed Jul 16 2014 - 22:00:02 PDT
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