[AMBER] Error : while running force field modification files

From: nalini chauhan <nalinichauhan.05.gmail.com>
Date: Thu, 6 Mar 2014 12:53:26 +0530

Respected Sir,

Since I am trying to parametrise my protein with attched zinc ion by
using MCPB. I have successfully run the files until force field
modification, however while running grep command for defining bond and
angles I am getting an error where bond and angles are undefined.

< Bond: |ZN|-|S3| 5.05401 0 0 2
< Bond: |ZN|-|S3| 2.82438 67.2006 0 2
< Bond: |ZN|-|N2| 5.55948 0 1 1
< Bond: |ZN|-|D1| 3.94011 0 0 1
< Angle: |CT|-|S3|-|ZN| 85.3487 -4.63872 1 2
< Angle: |CT|-|S3|-|ZN| 29.8465 -141.63 1 2
< Angle: |O2|-|C|-|D1| 51.4461 -8.80592 1 1
< Angle: |CR|-|N2|-|ZN| 83.8621 -257.525 1 1
< Angle: |S3|-|ZN|-|S3| 54.8796 17.2032 0 1
< Angle: |S3|-|ZN|-|N2| 40.5882 10.8406 0 2
< Angle: |S3|-|ZN|-|N2| 70.0116 -19.3068 1 2
< Angle: |S3|-|ZN|-|D1| 26.8667 52.3673 0 2
< Angle: |S3|-|ZN|-|D1| 36.5332 38.4371 0 2
< Angle: |N2|-|ZN|-|D1| 35.3865 -5.92273 1 1
< Angle: |C|-|D1|-|ZN| 102.204 -7.38445 1 1
< Angle: |CC|-|N2|-|ZN| 49.4866 -17.6567 1 1 
---
> Bond: |ZN|-|S3| Undefined
> Bond: |ZN|-|S3| Undefined
> Bond: |ZN|-|N2| Undefined
> Bond: |ZN|-|D1| Undefined
> Angle: |CT|-|S3|-|ZN| Undefined
> Angle: |CT|-|S3|-|ZN| Undefined
> Angle: |O2|-|C|-|D1| Undefined
> Angle: |CR|-|N2|-|ZN| Undefined
> Angle: |S3|-|ZN|-|S3| Undefined
> Angle: |S3|-|ZN|-|N2| Undefined
> Angle: |S3|-|ZN|-|N2| Undefined
> Angle: |S3|-|ZN|-|D1| Undefined
> Angle: |S3|-|ZN|-|D1| Undefined
> Angle: |N2|-|ZN|-|D1| Undefined
> Angle: |C|-|D1|-|ZN| Undefined
> Angle: |CC|-|N2|-|ZN| Undefined
command given by me was  :
    grep "Bond: |" protein_sidechain_fc_sem.bcl.log > protein_sem.txt;
    grep "Angle: |" protein_sidechain_fc_sem.bcl.log >> protein_sem.txt;
    grep "Bond: |" protein_sidechain_fc_md.bcl.log > protein_md.txt;
    grep "Angle: |" protein_sidechain_fc_md.bcl.log >> protein_md.txt;
    diff protein_sem.txt protein_md.txt
Also,I wanted to know that after running all the files in MCPB, I'll
be getting frmod & pdb files created by MCPB, so do i have to create
lib file for zinc and the bounded residues in leap??
Somehow I am not getting it.. Kindly look into the matter.
Thanks.
Regards,
Nalini
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Received on Wed Mar 05 2014 - 23:30:03 PST
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