Re: AMBER: ptraj problem

From: Thomas E. Cheatham, III <>
Date: Wed, 20 Aug 2003 13:00:57 -0600 (Mountain Daylight Time)

> I use ptraj to superimpose one MD trajectory for a diatomic molecule.
> I got this error message. It seems that it crashes when reading
> ANGLES_WITHOUT_HYDROGEN. In my case there is no angle. So, could you
> tell me how to fix this? Thanks.

There are two issues; one you need to get the bug fix to allow proper
reading of the new style prmtop (when no angles, etc are present). This
is available at I will
look into putting an appropriate bug fix on the AMBER WWW pages.

Second, RMSd fitting currently requires four atoms for a fit so it will
not allow RMS fitting a diatomic. The "principal" command may work, but I
don't know for sure. To use this,

   principal :1 dorotation

where your diatomic is residue 1 (:1).

Good luck,

\ 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: phone: (801) 587-9652 FAX: (801) 585-9119
\ Offices: BPRP295A / INSCC 418

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Received on Wed Aug 20 2003 - 20:53:01 PDT
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