[AMBER] missing parameter not present in antechamber generated frcmod

From: Sangita Kachhap <sangita.imtech.res.in>
Date: Wed, 19 Jan 2011 23:12:20 +0530 (IST)

Hello all

I have to generate parameter for phospho aspartate.
For this I have download sdf file for pohspho aspartate from PDB,converted it
into pdb
format using openbabel.

Using antechamber I have generated prepin file and to get the mising parameter
generate
frcmod file.In frcmod file there is only one missing parameter

remark goes here
MASS

BOND

ANGLE

DIHE

IMPROPER
c3-o -c -os 10.5 180.0 2.0 General improper
torsional angle (2 general atom types)

NONBON

When I load prepin and check the unit it shows missing parameter for

Checking for bond parameters.
Could not find bond parameter for: o - c
Could not find bond parameter for: c - h4
Could not find bond parameter for: c - c3
Could not find bond parameter for: c3 - n3
Could not find bond parameter for: c3 - h1
Could not find bond parameter for: c3 - c3
Could not find bond parameter for: n3 - hn
Checking for angle parameters.
Could not find angle parameter: o - c - h4
Could not find angle parameter: o - c - c3
Could not find angle parameter: c - c3 - n3
Could not find angle parameter: c - c3 - h1
Could not find angle parameter: c - c3 - c3
Could not find angle parameter: h4 - c - c3
Could not find angle parameter: c3 - n3 - hn


But in frcmod file their is not angle and bond parameter so I am not able to
generate parameter file.


When I repeat the same for ATP I successfully generate lib file and also prmtop
and inpcrd file for
protein having ATP.

So can anybody suggest me why missing parameters are not writing in frcmod file?


Here I am attaching following files:
  sdf
  pdb(converted by babel)
  prepin



With regard
Sangita Kachhap
JRF
BIC,IMTECH
CHANDIGARH

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Received on Wed Jan 19 2011 - 10:00:04 PST
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