Dear Amber Community,
I would like to compare the potential energy (PE) values of peptide
conformations that are generated in an MD trajectory and subsequently
energy-minimized, with the PE of the experimentally obtained (crystal or
solution) structure.
What is the recommended protocol for calculating "static" or single point
(potential) energy using AMBER (in order to obtain the PE of the
experimental structure)?
I tried this using energy minimization with parameters identical to those
used for post-MD minimization except for two changes: NTMIN changed from 1
to 2 and the number of iterations of steepest descent reduced to 10. The
initial energy, RMS and GMAX values (at NSTEP = 1) reported in the output
are high and positive. The input script I used is as follows:
&cntrl
imin = 1, ntmin = 2
maxcyc = 10,
ntb = 0,
igb = 1,
cut = 12
Is it correct to consider the initial energy as the PE of the conformation?
(Note: I have used Amber 9 and the simulations have been carried out using
GBSA solvent model.)
Thanks in advance for any help,
Sangeeta
--
This message has been scanned for viruses and
dangerous content by MailScanner, and is
believed to be clean.
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Wed Nov 08 2006 - 06:07:19 PST
