Dear Amber-Team,
I am dealing with a problem setting up a system in xleap/tleap (amber9) for some
time, but i have not been able to solve the problem on my own.
The goal is to set up a system with a different water model which is nicely
outlined in the manuscript and works well for all models except SPCFW water.
The datasets are included in the distribution. Following the guideline of the
manuscript i could not succeed - the simulation crashes.
After monitoring excatly all steps I decided to make a trial run using the pure
SPCFWBOX (containg 216 waters) but still i had no success.
The syntax I used to set up this system is essentially very simple (and as
mentiond works well for all other water and non-water models):
source leaprc.ff99
WAT = SPF
loadAmberParams frcmod.spcfw
saveAmberParm SPCFWBOX spcfw.prmtop spcfw.inpcrd
quit
Taking a look at the resulting prmtop file I receive the following system
description:
%FLAG POINTERS
%FORMAT(10I8)
648 2 648 0 0 0 0 0 0 0
864 216 0 0 0 2 0 0 2 1
0 0 0 0 0 0 0 1 3 0
0
Luckily, exactly the same system is one of the test runs found in
$AMBERHOME/test/pimd_spcfw/.
The prmtop-file of this example (spcfw.top) has a different entry:
%FLAG POINTERS
%FORMAT(10I8)
648 2 648 0 216 0 0 0 0 0
864 216 0 0 0 2 1 0 2 1
0 0 0 0 0 0 0 1 3 0
0
The differences are apperently related to the angles (which is also seen from
the simulation - all H-O-H angles become zero and the associated hydrogens
"merge"). Utilising the correct prmtop file taken from the test-run for my
trial jobs results in nice minimisations and md-runs of the pure water system
including water flexibility.
Unfortunately, no leap.log or other help is found in $AMBERHOME/test/pimd_spcfw/
to explain how to motivate xleap/tleap to include the angle data in the prmtop
file. As my target systems have (of course) a significant complexity it is not
feasible to modify the prmtops manually after the leap-setup.
I would kindly appreciate any help on this problem.
With best regards and thanks in advance,
Thomas Hofer
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Received on Sun Jun 24 2007 - 06:07:58 PDT
