AMBER Archive (2003)

Subject: Re: about molecular dynamics

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Tue Apr 29 2003 - 22:30:06 CDT

Ronnie,
your file has this for the restraint info:

# 6 GUA H8 5 CYT H1' 0.000

&rst

ixpk= 0, nxpk= 0, iat= 173, 140, r1= 1.30, r2= 1.80, r3= 0.00, r4= 0.50,
&end

#

# 6 GUA H8 5 CYT H3' 3.914

&rst

your r3 for this restraint is actually 0, not 3.47 as you said in your mail.
check the file again and let me know if fixing this doesn't solve
it.
good luck
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
===================================================================

----- Original Message -----
From: "ronnie" <s020405_at_mailserv.cuhk.edu.hk>
To: <amber_at_heimdal.compchem.ucsf.edu>
Sent: Tuesday, April 29, 2003 9:09 PM
Subject: about molecular dynamics

> Hello,
>
> When i am running the Molecular dynamics simulated annealing in vacuum
with
> distance constraints (7col.dist), there is an error : r1 -> r4 (and r1a ->
> r4a) must be monotonically increasing; Offending restraint:
> ******
> H8 ( 173)-H1' ( 140) NSTEP1= 0 NSTEP2 =0
> R1=1.300 R2=1.800 R3=0.000 R4=0.500
>
> But when I look into the RST.dist
> there is:
> r1=1.30, r2=1.80, r3=3.47, r4=3.97.
>
> Can I have any help to solve this problem?
>
> yours, Ronnie
>
>