AMBER Archive (2004)

Subject: Re: AMBER: Trouble running molecular dynamics with an increase in temp in Sander

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Wed Jun 16 2004 - 09:42:33 CDT

there is a problem in your input. look at the sander output
where it says:

> 5. REFERENCE ATOM COORDINATES
>
>
> ----- READING GROUP 1; TITLE:
> &rst
>
> GROUP 1 HAS HARMONIC CONSTRAINTS -4.00000
> GRP 1 RES 1 TO 30
> Number of atoms in this group = 991
> ----- END OF GROUP READ -----
>

it's always a good idea to read your output file carefully.
it clearly is not reading your positional (ntr=1) restraints properly, it
is using the &rst lines as your GROUP input for positional restraints.

according to page 119 of the AMBER8 manual (the section on restraints),
"unlike earlier versions of AMBER, the &rst namelists must be in the
DISANG file and not in the mdin file"

the paragraph right above that one tells you how to do weight changes
without
restraints. the bottom line is that your input should work fine if
you remove the &rst section from your input.

carlos
===================================================================
Carlos L. Simmerling, Ph.D.
Assistant Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
Stony Brook University Web: http://comp.chem.sunysb.edu/carlos
Stony Brook, NY 11794-5115 E-mail: carlos.simmerling_at_stonybrook.edu
===================================================================

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