Hi Thomas,
Leap is removing the angle terms because it thinks you want rigid water -
the default since it assumes you use shake. For SPCFW you need the angle
terms since you won't be using shake and you'll have a smaller timestep (ca
1fs). So try the following in leap before you do the solvation:
set default FlexibleWater on
Then try the solvation and save your prmtop file.
>From Page 67 of the manual:
FlexibleWater If set to "on", LEaP will not remove the HW-OW-HW angle from
water
residues; if set to "off" (the default), LEaP will remove this angle. In all
cases, the HW-HW-OW angle in water residues is removed if it is present.
As the name suggests, you should turn this variable "on" if you are using a
flexible water model.
Good luck...
Ross
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|\oss Walker
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> -----Original Message-----
> From: owner-amber.scripps.edu
> [mailto:owner-amber.scripps.edu] On Behalf Of Thomas Hofer
> Sent: Saturday, June 23, 2007 09:03
> To: amber.scripps.edu
> Subject: AMBER: SPCFW water: angle problems in leap
>
> 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
