normal bbsc.sh script - errors

  • poojaric
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11 months 3 weeks ago #8273 by poojaric
bbsc.sh script - errors was created by poojaric
Dear All,

I have a protein with several chains. After generating coarse grained itp file with martinize file provided with martini 3 package, I ran the following command:

./bbsc.sh Protein_CG.itp Protein_AA.pdb

However, I got the below error message:
:./bbsc.sh: line 12: vmd: command not found

To overcome this, i gave full path to vmd inside bbsc.sh script and now i get this message, but the Protein_CG.itp is updated now.
/usr/local/lib/vmd/vmd_LINUXAMD64: /usr/lib/x86_64-linux-gnu/libGL.so.1: no version information available (required by /usr/local/lib/vmd/vmd_LINUXAMD64)

The Protein_CG.itp file is updated as shown below.

ERROR reading the topology Protein_CG.itp
.
.
moving CA and CB to center of mass of BB, SC1 bead
ERROR: did not recognize residue ASN ASN ASN
ERROR: did not recognize residue ALA ALA ALA
.
.
measuring SC BB BB SC dihedrals
[ dihedrals ]
; SC-BB-BB-SC dihedrals
2 1 3 4 1 -180 100 1 ; N(1)-I(2)
.
.
512 511 513 514 1 -180 100 1 ; C(212)-S(213)
expected integer but got ""



Please can I Know what I may be doing wrong with my input files. Any suggestions will be very helpful. Also pasted are the contents from bbsc.sh script.

#####################################################
#!/bin/bash
if "$#" != 2
then
echo "Arguments must be <itp> <aa-pdb>" >&2
exit 1
fi

itp=$1
pdb=$2

{
/usr/local/vmd -dispdev text -eofexit << EOF
source addDihedral.tcl
addDihedral $itp $pdb
EOF
} | grep -v Info | grep -v vmd | tail -n+4 >> $itp


#####################################################



Kind Regards,
Chetan

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  • peterkroon
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11 months 3 weeks ago #8276 by peterkroon
Replied by peterkroon on topic bbsc.sh script - errors
> /usr/local/lib/vmd/vmd_LINUXAMD64: /usr/lib/x86_64-linux-gnu/libGL.so.1: no version information available (required by /usr/local/lib/vmd/vmd_LINUXAMD64)

Your VMD is broken. It might get fixed if you reboot your computer due to graphics drivers, but I can't and won't try to debug further from here.

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11 months 3 weeks ago #8278 by poojaric
Replied by poojaric on topic bbsc.sh script - errors
Dear Peter,

The problem was not with the vmd installation.

My protein is a trimer and chains are labelled differently. Also the residues are not numbered consecutively. On having same chain label and numbering the residues consecutively everything worked fine and I did not have any error message in my itp file.

Kind Regards,
Chetan

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