AMBER Archive (2003)

Subject: Re: AMBER: question about ptraj?

From: Thomas E. Cheatham, III (cheatham_at_chpc.utah.edu)
Date: Thu Jul 24 2003 - 11:40:50 CDT

> I try to do some trajectory analysis for the ligand which is bound to
> a protein. I use ptraj to get the trajectory for the ligand from a MD
> result. But I find a strange thing. This is the input file I use:
>
> trajin md_nvt4_now_fit.crd
> strip :970-976
> strip :1-968
> trajout test.crd
> go
>
> The ligand is residue #969. If I use this input file, I can get right
> output (trajectory). But If I switch two 'strip' lines which means I
> strip residue 1-968 first then 970-976. The program complains that it
> can not find residue 970-976. Then the output file includes residue
> 970-976. Any clue? And if I want to keep some residues in the active
> site. What should I do? How can I strip them correctly?

What happens is that after the strip :1-968 (if this is done first)
is that the residues are effectively renumbered so that now :969 is
residue :1.

What you show about should work, i.e. strip that higher numbered residues
first.

Alternatively,

strip :1-968,970-976

or

strip ^:969

Finally with the trajout command below you might want to add the
"nobox" command to avoid writing box information to the trajectory.

Good luck and let me know of further problems,

\ Thomas E. Cheatham, III (Assistant Professor) College of Pharmacy
| Departments of Medicinal Chemistry and of University of Utah
| Pharmaceutics and Pharmaceutical Chemistry 30 South 2000 East, Room 201
| & Center for High Performance Computing Salt Lake City, Utah 84112
|
| e-mail: tec3_at_utah.edu phone: (801) 587-9652 FAX: (801) 585-9119
\ http://www.chpc.utah.edu/~cheatham Offices: BPRP295A / INSCC 418

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