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. 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
BOND
OW-HW 0.00 0.000 ATTN, need revision
ANGLE
HW-OW-HW 0.000 0.000 ATTN, need revision
DIHE
IMPROPER
NONBON
OW 1.7210 0.2104 same as oh
HW 0.0000 0.0000 ATTN, need revision
>Does it mean that the angle parameter for H-O-H is not found?
>And what should I do to fix this problem? Would you like give me some help? Thanks!Thanks alot
Best Regards, Saman Yousuf AliJunior Research Fellow,
| Lab No. P-133, Computational Chemistry Laboratory
Dr. Panjwani Center for Molecular Medicine & Drug Research,
International Center for Chemical & Biological Sciences,
University of Karachi – 75270.Karachi-Pakistan.
Contact No:
Office (92-21) 111222292 (Ext 309)
Email ID: saman.yousufali64.yahoo.com
saman.ali.iccs.edu
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Received on Fri Jan 22 2016 - 03:30:02 PST
