AMBER Archive (2001)

Subject: Re: (No Subject)

From: Jarrod Smith (jsmith_at_reef.structbio.vanderbilt.edu)
Date: Thu Mar 08 2001 - 13:59:36 CST

Anwer Mujeeb wrote:
>
> Hello:
>
> The problem i see is in flat-well part of the restraint. The r3 value is
> less than r2 value (1.8). This should be in increasing order from
> r1-to-r4. At that point r2 and r3 will define the flat part of the well.
> hope this helps.

Sorry if my answer wasn't clear. This is what I was getting at. The
person who posed this question would need to modify makeDIST_RST so that
r2 will be smaller than the smallest upper bound of the input file. But
in terms of the AMBER forcefield, it isn't very realistic to use upper
bounds smaller than 1.8 because you are building bad restraint (and VDW)
energy into your system. 

-- 
Jarrod A. Smith
Research Asst. Professor, Biochemistry
Asst. Director, Center for Structural Biology
Computation and Molecular Graphics
Vanderbilt University

jsmith_at_structbio.vanderbilt.edu