vmd.cna error

[Gauri Thapa]

I am trying to visualize my results with VMD. When I type the following command

vmd.cna(net_cutoff0.6, pdb, )

I get the following error.

Error in vec2resno(vec = x$communities$membership, resno = pdb$atom[, : Length miss-match of 'vec' and concetive 'resin'

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pdb

Call: read.pdb(file = "../b_no_water.pdb")

Total Models#: 1
Total Atoms#: 632, XYZs#: 1896 Chains#: 2 (values: C K)

 Protein Atoms#: 630  (residues/Calpha atoms#: 157)
 Nucleic acid Atoms#: 0  (residues/phosphate atoms#: 0)

 Non-protein/nucleic Atoms#: 2  (residues: 2)
 Non-protein/nucleic resid values: [ CAL (2) ]

Protein sequence:
DQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNG
TIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEV
DEMIREADIDGDGQVNYEEFVQMMTAAWASLKRLVTR

• attr: atom, xyz, calpha, call

net_cutoff0.6

Call:
cna.dccm(cij = cij, cutoff.cij = 0.6)

Structure:

• NETWORK NODES#: 157 EDGES#: 962

• COMMUNITY NODES#: 9 EDGES#: 11

• attr: network, communities, community.network,
  community.cij, cij, call

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[Xinqiu Yao]

Hi,

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It might be because the residue number is repeated in the two chains. Renumber residues using clean.pdb(pdb, force.renumber=TRUE) or convert.pdb(pdb, renumber=TRUE) and try again.

[Gauri Thapa]

Hi,

Thank you so much.

I tried both the command and still getting the error. I even renumbered the repeating residue number so that the residue number is not repeated and tried using vmd.cna but still getting the same error.

Thanking you

[Xinqiu Yao]

Can you provide a short example that can reproduce the problem? Then, I can take a look.

[Gauri Thapa]

The commands that I used are

pdb<-read.pdb(“b_no_water.pdb”)

inds<-atom.select(pdb, elety=”CA”)

cij<-read.table(“lmi.txt”)

cij<-data.matrix(cij)

net_cutoff0.5<-cna(cij, cutoff.cij=0.5)

vmd.cna(net_cutoff0.5, pdb)

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[Gauri Thapa]

And after your suggestions ,

vmd.cna(net_cutoff0.5, clean.pdb(pdb, force.renumber=TRUE))

I also changed the residue numbers in the pdb file as given in b_resno_new.pdb and redid the calculation ,again getting the same error.

Thank you so much for your help.

[Gauri Thapa]

The residues were repeated in the segname KC in the pdb file which I have changed in b_resno_new.pdb.

[Xinqiu Yao]

The pdb has non-protein atoms that should be cleaned out before calling vmd.cna(). Try vmd.cna(net_cutoff0.5, clean.pdb(pdb, force.renumber=TRUE, rm.lig=TRUE))

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[Gauri Thapa]

Hi,

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Thank you so much for all your help. Now it is working.

[Mark Long]

Hi Xinqiu Yao,

vmd.can() does not recognize non-standard amino acid. e.g. vmd.can() does not recognize phosphorylated aspartic (PHD) acid residue. After I replaced PHD with ASP in PDB file (just change residue name), vmd.can() can works well. I hope that my feedback can help me to improve your software.

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[Xinqiu Yao]

Thanks for the feedback! Will put it on the to-do list for the next release shortly.

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[Xinqiu Yao]

Add features in vmd.cna() to recognize non-standard amino acid residues.