AMBER Archive (2000)

Subject: Re: Saving coordinates with sander_classic

From: Michael Cooney (mike_at_bmbiris.bmb.uga.edu)
Date: Thu Dec 21 2000 - 15:34:34 CST

Dear Dr. Philippopoulos:

I think you need to include

ntwvm=0, ntwem=0, ntwxm=0,

in your input file, to disable the default limits on coordinate/velocity/
energy writing.
I hope this helps. Good luck!

Sincerely,
Michael Cooney
Department of Biochemistry and Molecular Biology
The University of Georgia
Athens, GA 30602
 

On Wed, 6 Dec 2000, Marios Philippopoulos wrote:

> Hi everyone,
>
> I have been running the following script with sander_classic, and I just
> noticed that no
> coordinates are written out in the mdcrd file. I used the "-x mdcrd"
> option when invoking
> sander_classic, and NTWX=2000. Can somebody find the problem?
> Thanks,
>
> Marios Philippopoulos
>
> Here is the mdin file:
>
> &cntrl
> init=4,
> imin=0, irest=1, ntx=5, idiel=0,
> ntt=1, tempi=5000., temp0=5000., tautp=1.0,
> ntb=0, ntr=1, ibelly=1, scee=1.2, cut=9.0,
> ntc=2, tol=0.00001, dt=0.0005, ntf=2, ntcm=1,
> nstlim=100000, ntwx=2000, ntpr=250,
> &end
> Harmonically restrain sidechains:
> 10.0
> FIND
> * * S *
> * * B *
> * * 3 *
> * * E *
> SEARCH
> RES 1 7
> RES 9 27
> RES 29 31
> RES 33 100
> END
> Harmonically restrain sidechains:
> 25.0
> FIND
> * * S *
> * * B *
> * * 3 *
> * * E *
> SEARCH
> RES 8
> RES 28
> RES 32
> RES 104
> END
> END
> Fix protein backbone:
> FIND
> * * M *
> * H E *
> * O E *
> SEARCH
> RES 1 100
> END
> END
>
> --
> Marios Philippopoulos, PhD
> Structural Biology and Biochemistry Programme
> Hospital for Sick Children
> 555 University Avenue
> Toronto Ontario Canada M5G 1X8
>
> mphilip_at_sickkids.on.ca
>
>
>