AMBER Archive (2001)

Subject: Re: Serious Problem with parm99.dat

From: jim caldwell (caldwell_at_heimdal.compchem.ucsf.edu)
Date: Fri Jan 26 2001 - 14:18:51 CST

This affect the verion of Parm99 posted on the
Amber web page and the parm99.datfile (possibly)
distributed with Amber5.

Make the following substitions

536,538c536,538
< C -CT-N -C 1 0.50 180.0 -4. phi,psi,parm94
< C -CT-N -C 1 0.15 180.0 -3. phi,psi,parm94
< C -CT-N -C 1 0.53 0.0 1. phi,psi,parm94 

---
> CT-CT-N -C    1    0.50        180.0            -4.         phi,psi,parm94
> CT-CT-N -C    1    0.15        180.0            -3.         phi,psi,parm94
> CT-CT-N -C    1    0.53          0.0             1.         phi,psi,parm94

( the "<" lines are to be removed and replaced with ">" lines)

jim

On Fri, 26 Jan 2001, JUNMEI Wang wrote:

> Hi, Warren,
>   I checked the origin files and I found that it is a type error of 
> parm99.dat in the web. It should be CT-CT-N-C, not C-CT-N-C. My old 
> versions of parm99.dat are all correct. This error was introduced recently 
> during the procedure of reorgnizing/revising the file. 
>   The simulations on the paper are all fine. 
>   As I know, the parm/leap program can wisely ignore redundant parameters
> (the priority order is as the following: specific parameter in frcmod >
> general parameter in frcmod >specific parameter in parm9x >general
> parameter in parm9x).
>   I am sorry for this serious problem. 
>  
> Junmei 
> 
> 
> -----------------------------------------
> Junmei Wang, Ph.D.  
> Department of Pharmaceutical Chemistry, 
> University of California San Francisco,
> San Francisco, CA 94143-0446
> Phone: (415)476-7900 (lab)
>        (415)681-7818 (home)
> Fax:   (415)502-1411
> Email: junmei_at_cgl.ucsf.edu 
> -----------------------------------------
> 
> 
> 

----------------------------------------------------------------------------
James W. Caldwell                         (voice) 415-476-8603
Department of Pharmaceutical Chemistry    (fax)   415-502-1411  
Mail Stop 0446                            (email) caldwell_at_heimdal.ucsf.edu
513 Parnassus Avenue                      (video) farbauti.compchem.ucsf.edu 
University of California                          (netmeeting) 
San Francisco, CA 94143-0446               
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