[AMBER] Error: A residue defined as a "fast 3-point water"

From: Saman Yousuf ali <saman.yousufali64.yahoo.com>
Date: Fri, 22 Jan 2016 11:28:34 +0000 (UTC)

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
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