On Fri, Jan 22, 2016 at 6:28 AM, Saman Yousuf ali <
saman.yousufali64.yahoo.com> wrote:
> Dear all,
>
> In AMBER12, My target protein active site includes NADPH, and a number of
> crystal waters. These waters may influence the interaction among NADPH with
> ligand and surrounding amino-acid residues. When I carried out
> minimization, while holding a part of the system restrained, the mdout file
> gives the following error message >begin time read from input coords =
> 0.000 ps
>
> > Error: A residue defined as a "fast 3-point water"
> is not defined by a triangle of three bonds.
> Residue 539 contains 2 bonds.I have also prepared
> water prepin and frcmod for making active site water molecule different
> from TIP3P water box molecules.
Why are you doing this? I would highly recommend against it. Unless the
water is covalently bound to a ligand, it does not make sense to use
different models for different water molecules in your system. After all,
if the water molecules exchange (which they *should*), then your "mutant"
waters simply become diluted in the bulk solvent.
> Parameter files for crystal water are attached below,
> > wat.prepin
> 0 0 2
>
> This is a remark line
> molecule.res
> WAT XYZ 0
> CHANGE OMIT DU BEG
> 0.0000
> 1 DUMM DU M 999.000 999.0 -999.0 .00000
> 2 DUMM DU M 999.000 -999.0 999.0 .00000
> 3 DUMM DU M -999.000 999.0 999.0 .00000
> 4 O ow M -12.645000 16.066000 13.679000 -0.785000
> 5 H1 hw E -11.688000 16.066000 13.679000 0.392000
> 6 H2 hw E -12.885000 16.993000 13.679000 0.392000
>
>
> LOOP
>
> IMPROPER
>
> DONE
> STOP
> >wat.frcmod
> remark goes here
> MASS
> OW 16.000 0.465 same as oh
> HW 0.000 0.000 ATTN, need revision
>
Here you define atom types HW and OW, but in the prepin file, you use gaff
atom types ow and hw. I'm really not sure how this ever worked in tleap,
or if it did, what was even done. Your prep file probably overwrote the
WAT residue defined for tip3p with GAFF atom types, in which case this
frcmod file (which is wrong, since you need to actually fix the lines that
say "ATTN, need revision") actually does not do anything.
There are many problems with your files here. The root of them -- trying
to assign different parameters to different water molecules -- seems to be
at the root of these problems. So don't do that. Just let tleap treat all
waters the way it wants to treat waters. If you have a good reason *not*
to do this, then you'll need to explain more detail exactly what you are
trying to do.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Jan 22 2016 - 05:00:05 PST
