On Wed, Sep 22, 2010, Anthony Costa wrote:
>
> I have done that, and everything seemed to be fine, until I actually
> looked at the topology while using a flexible water parametrization.
> The frcmod information doesn't seem to be being applied at all.
>
> PDB:
> [...]
> ATOM 1 O WAT 1 75.670 75.870 35.030 1.00 0.00
> ATOM 2 H1 WAT 1 75.750 75.690 36.010 1.00 0.00
> ATOM 3 H2 WAT 1 74.720 75.780 34.750 1.00 0.00
> ATOM 4 O WAT 2 79.110 75.960 33.670 1.00 0.00
> ATOM 5 H1 WAT 2 78.690 76.830 33.930 1.00 0.00
> ATOM 6 H2 WAT 2 78.430 75.390 33.210 1.00 0.00
> [...]
>
> TLEAP:
> source leaprc.ff03.r1
> loadamberparams frcmod.spcfw
> WAT = SPF
> CLUSTER = loadpdb conf.pdb
> saveamberparm CLUSTER conf.top conf.crd
> quit
Remember that for flexible waters, you have to issue the instruction
"set default FlexibleWater on"; otherwise LEaP assumes that you have a rigid
water, and removes all of the angle terms.
[To developers: this is a very easy thing to miss, but I don't see a good way
to automatically set this parameter; could loading a flexible water frcmod
somehow trigger the right behavior automagically?]
....dac
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Received on Wed Sep 22 2010 - 13:30:09 PDT
