AMBER Archive (2003)

Subject: glycam force field with amber

From: PSR04996_at_mailstudenti.unimi.it
Date: Fri Jun 13 2003 - 06:28:07 CDT

Dear all,
 
  I'm performing molecular dynamic simulations of an enzyme in presence
of its substrate. The last one is a sugar (monosaccaride)composed of
more or less 45 atoms. Owing to the presence of the sugar it is
necessary to use the glycam force field (2000 version by Woods et al.)
in addition to the 'normal' amber7 force field (parm99). Performing an
equilibration dynamic on the solvated enzyme alone (without the sugar
and without the need of using glycam) requires more or less 30 hours
for a 50ps long dynamic on a Pentium4 180Mhz machine. When we add the
sugar (with an increase in size of the system of 45 atoms over more
than 20000), a dramatic increase of computing time is observed (five
times). We searched the reason of these increase in the computation of
hidrogen bonds, but we think these are calculated only between the
sugar and the surrounding molecules, and not between all the atoms.
Another explanation could be a problem of compatibility between amber7
and glycam2000. We would be very pleased to know your opinion about
this problem and the reasons that could cause it.

                                  Thank you in advance for your help

                         Stefano Pieraccini