Subject: generating .crd from IC in CHARMM

From: Charles McCallum <[email-masked]>
Date: Sun, 23 Mar 2003 10:19:00 -0800

One of my students asked me a question about generation of cartesian 
coords from ICs in CHARMM (c27b4), and I couldn't answer it.  When 
generating a DPPC in a three-residue (PALM, PCGL, PALM) way, we have 
been reading in an existing .crd file to specify the cartesian coords.  
The question was:  "can't the ICs determine a set of cartesian coords?" 
  We tried it, and what happens using the "ic seed" command is we get 
cartesians for only the residue that the seed atoms belong to.  I've 
put an illustrative input file and the resulting .crd file here:

http://onsager.cop.uop.edu/~mccallum/group-files/test.inp
http://onsager.cop.uop.edu/~mccallum/group-files/ss01dppc.crd

Can anyone explain to me why we're not getting a full set of coords?

A second question regards the new version of CHARMM - c29.  How useful 
will an upgrade be to us?  WE run mostly aqueous amphiphilic and 
protein simulations, and must generate some of our own parameters.

Cheers,

Mike McCallum
--
C. Michael McCallum                        
http://chem.cop.uop.edu/cmmccallum.html
Associate Professor
Department of Chemistry, UOP
mmccallum .at. uop . edu                (209) 946-2636 v  / (209) 
946-2607 fax