VMD-L Mailing List

From: PRITI ROY (priitii.roy_at_gmail.com)
Date: Sun Aug 04 2019 - 01:51:30 CDT

Dear experties,
I would like to calculate the network analysis by considering a residue
(only heavy atoms) as node for a dimeric protein system.

Here is the input of networkSetup:
##############################
>Psf
protein.psf

>Dcds
protein.dcd

>SystemSelection
(chain A B) and (not hydrogen)

>NodeSelection
(resname SER LEU GLU CYS ASP PRO ALA VAL ILE GLY THR LYS HSE TYR TRP ASN
ARG MET GLN PHE and name CA)

>Clusters
CA SER name N CA CB OG C O
CA LEU name N CA CB CG CD1 CD2 C O
CA GLU name N CA CB CG CD OE1 OE2 C O
CA CYS name N CA CB SG C O
CA ASP name N CA CB CG OD1 OD2 C O
CA PRO name N CA CB CG CD C O
CA ALA name N CA CB C O
CA VAL name N CA CB CG1 CG2 C O
CA ILE name N CA CB CG1 CG2 CD C O
CA GLY name N CA C O
CA THR name N CA CB OG1 CG2 C O
CA LYS name N CA CB CG CD CE NZ C O
CA HSE name N CA CB CG CE1 NE2 CD2 C O
CA TYR name N CA CB CG CD1 CD2 CE1 CE2 CZ C O
CA TRP name N CA CB CG CD1 NE1 CE2 CD2 CE3 CZ3 CZ2 C O
CA ASN name N CA CB CG OD1 ND2 C O
CA ARG name N CA CB CG CD NE CZ NH1 NH2 C O
CA MET name N CA CB CG SD CE C O
CA GLN name N CA CB CG CD OE1 NE2 C O
CA PHE name N CA CB CG CD1 CE1 CZ CD2 CE2 C O

>Restrictions
notSameResidue
####################################################

and it is giving the following error:
"can't read "nodeMap(1865)": no such element in array"

Though I was able to generate the networkView based on CA atom. For residue
wise calculation I also tried by setting" NodeSelection as residue" but in
the out file each of the heavy atom considered as node. Then I took the
above approach.

Any suggestions would be highly appreciated for this problem.

Thanking you,
Priti Roy