Subject: Standalone CHARMm help!

From: Hu LiHong <[email-masked]>
Date: Mon, 21 Oct 2002 21:41:17 +0800 (HKT)

Dear all,

I have tried CHARMM calculation many times, there are always some problem 
happened. Who has used the CHARMM to calculate protein can share some 
experience with me. In my calculation, I feel CHARMM is a terrible 
program. The total energy calculated by sd and abnr have so much 
difference I can't imagine. I don't know what wrong with it.

I want to consult a CHARMM expert about protein calculation.

1. I want to use QM/MM calculate protein to get binding energy between a 
ligand (about 30 atoms) and a protein (about 5300 atoms). Can I realize my 
calculation by standalone CHARMM 27.3 version? What keywords I should 
choose? (I knew I should use 'quan sele segi qm-atoms end method' for qmmm 
calculation) Can I find the binding energy in the qmmm calculation 
output file directly? (I mean just plus some energy terms to get the 
binding energy of two part.)
 
2. In QMMM calculation, should I minimize the structure of protein? If 
yes, I should minimize it before qmmm calculation or after qmmm 
calculation? Which minimization method should I choose? Until now, I have 
use SD and ABNR, both don't work well, SD is noconvergent method, I get 
energy (-19000 or so by 10000 nstep), but ABNR energy is (+1.4*E+61), is 
it horrible? And in the output files there are "Maximum group spatial 
extent (12A) exceeded" complainted, how can I extend the group boundary?

3. Could you provide me a sample input file for protein qmmm 
calculation not for small molecule? I attach my input file and Could you 
correct the mistake for me?

I am very appropriated your great help,

Best Wishes,

Carol