AMBER Archive (2002)

Subject: belly input

From: Prabal Maiti (maiti_at_wag.caltech.edu)
Date: Tue Feb 12 2002 - 16:26:21 CST


As I was going through excellent step by step introduction as to how to
use AMBER for DNA simulation in tutorial section of AMBER home page I came
accross the following situation

I looked at atA.topo atA.topo.belly files and when I diff them I get

< 38 2883 3
< 319 319 1 1 1 1 1 1 1 1 1 1
< 1 1 1 1 1 1 1 1 3 3 3 3

---
>     38  2882     3
>    638     1     1     1     1     1     1     1     1     1     1     1
>      1     1     1     1     1     1     1     3     3     3     3     3
13807c13807
<      3     3     3
---
>      3     3
 

In the explanation below it is said that I should decrement NSPM by 1 and NSPSOL by 1. So 2883 is dcremented by 1 but 3 is not dcrement by 1. Is that a typo or there is some more to it.

>To modify the topology file, you decrement NSPM by 1 and NSPSOL by 1 >then >take the first two entries in the molecule array that follows and >add them together. Replace the first entry with this value, delete the >second and shift the molecule array back. You can follow the molecule >array since it is filled with 3's which represent the water. This all >perhaps sounds crazy, perhaps a little overkill, and perhaps a waste of >time to >present, however this is what I do to get belly to work for >equilibration. You can "diff" (or gdiff on the SGI's) the two files to >get >a better idea of >what I am talking about...

I need to resolve it before making a belly topology file for my simulation.

Prabal

-- ------------------------------------------------------------------------ Prabal K Maiti Email:maiti_at_wag.caltech.edu Beckman Institute (139-74) pkmaiti_at_yahoo.com California Institute of Technology Tel:626-395-8151 (O) 400 South Wilson Avenue :626-744-1363 (H) Pasadena, CA 91125 Fax:626-585-0918 Home add: 110 S. Michigan Ave. http://www.wag.caltech.edu/home/maiti Apt # 19, Pasadena, CA 91106 ------------------------------------------------------------------------