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bbsc.sh script - errors
- poojaric
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4 years 6 months 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 >> $itp
#####################################################
Kind Regards,
Chetan
I have a protein with several chains. After generating coarse grained itp file with martinize file provided with martini 3 package, I ran the following command:
./bbsc.sh Protein_CG.itp Protein_AA.pdb
However, I got the below error message:
:./bbsc.sh: line 12: vmd: command not found
To overcome this, i gave full path to vmd inside bbsc.sh script and now i get this message, but the Protein_CG.itp is updated now.
/usr/local/lib/vmd/vmd_LINUXAMD64: /usr/lib/x86_64-linux-gnu/libGL.so.1: no version information available (required by /usr/local/lib/vmd/vmd_LINUXAMD64)
The Protein_CG.itp file is updated as shown below.
ERROR reading the topology Protein_CG.itp
.
.
moving CA and CB to center of mass of BB, SC1 bead
ERROR: did not recognize residue ASN ASN ASN
ERROR: did not recognize residue ALA ALA ALA
.
.
measuring SC BB BB SC dihedrals
[ dihedrals ]
; SC-BB-BB-SC dihedrals
2 1 3 4 1 -180 100 1 ; N(1)-I(2)
.
.
512 511 513 514 1 -180 100 1 ; C(212)-S(213)
expected integer but got ""
Please can I Know what I may be doing wrong with my input files. Any suggestions will be very helpful. Also pasted are the contents from bbsc.sh script.
#####################################################
#!/bin/bash
if "$#" != 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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4 years 6 months 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.
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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- poojaric
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4 years 6 months 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
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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- aishwaryts
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3 years 6 months ago #8729
by aishwaryts
Replied by aishwaryts on topic bbsc.sh script - errors
My AA pdb file is correctly lableled (chains and residue numbers)
I was wondering if anyone got this issues while running bbsc.sg script
load pdb file mdm2-p53.pdb
moving CA and CB to center of mass of BB, SC1 bead
ERROR: did not recognize residue GLU LEU
ERROR: did not recognize residue THR LEU
ERROR: did not recognize residue LEU PRO
ERROR: did not recognize residue VAL GLU
ERROR: did not recognize residue ARG ASN
ERROR: did not recognize residue GLU LEU
ERROR: did not recognize residue THR LEU
ERROR: did not recognize residue LEU PRO
ERROR: did not recognize residue VAL GLU
ERROR: did not recognize residue ARG ASN
measuring SC BB BB SC dihedrals
Regards,
Aishwary
I was wondering if anyone got this issues while running bbsc.sg script
load pdb file mdm2-p53.pdb
moving CA and CB to center of mass of BB, SC1 bead
ERROR: did not recognize residue GLU LEU
ERROR: did not recognize residue THR LEU
ERROR: did not recognize residue LEU PRO
ERROR: did not recognize residue VAL GLU
ERROR: did not recognize residue ARG ASN
ERROR: did not recognize residue GLU LEU
ERROR: did not recognize residue THR LEU
ERROR: did not recognize residue LEU PRO
ERROR: did not recognize residue VAL GLU
ERROR: did not recognize residue ARG ASN
measuring SC BB BB SC dihedrals
Regards,
Aishwary
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- jessicab
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2 years 8 months ago #9090
by jessicab
Replied by jessicab on topic bbsc.sh script - errors
The problem arises because the pdb contains multiple chains. I also had the same issue and noticed that the residue name is printed twice in the error. It encounters it once in chainA and again in chainB.
You can fix this by making separate pdb files for chainA and chainB and then running the command -
./bbsc Protein_A.itp chainA.pdb
./bbsc Protein_B.itp chainB.pdb
This makes sense since Protein_A.itp only has the topology of one chain.
-Jessica
You can fix this by making separate pdb files for chainA and chainB and then running the command -
./bbsc Protein_A.itp chainA.pdb
./bbsc Protein_B.itp chainB.pdb
This makes sense since Protein_A.itp only has the topology of one chain.
-Jessica
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