From: Aliakbartehrani Zahra (Zahra.Aliakbartehrani_at_ibt.cas.cz)
Date: Mon Nov 25 2019 - 04:56:22 CST

Dear all,

I am using dynamical network analysis on top of my MD simulation Traj files for 5 different ligands interacting with the same protein (300ns simulation in AMBER, with .dcd and .top files converted to .psf file with CPPTRAJ) by using the following network.config file (including CA of residues in the protein and 4 nodes per ligand (residue called SDF with cyclic AMP-based structure).

>Psf

/storage/plzen1/home/zahratehrani7/network-analysis/complex-1/Nowat_sdf.psf

>Dcds

/storage/plzen1/home/zahratehrani7/network-analysis/ complex-1/sdf-Sup.dcd

>SystemSelection

all and (not hydrogen)

>NodeSelection

(name CA ) or (resname SDF and name N14) or (resname SDF and name N37) or (resname SDF and name P1) or (resname SDF and name P25)

>Clusters

N14 SDF name N14 N22 C21 N20 C18 O19 C17 N23 C24 N16 C15 N14

N37 SDF name N37 C38 N39 C40 C47 N37 C41 N43 C44 N46 N45 O42

P1 SDF name P1 C13 C11 O12 C9 O8 C7 C6 O5 O3 O33 O4

P25 SDF name P25 O26 O10 O27 O28 C29 C30 C32 C34 O35 O31 C36

>Restrictions

notSameResidue

notNeighboringCAlpha

notNeighboringPhosphate

calculations converged with no error but when I have tried to load contact.dat file into protein-ligand-complex.pdb/.psf file in networkView got this error (only for 2 out of 5 ligands):

Error: number of nodes (369) does not agree with adjacency matrix rank (372)

The system has 369 residues including the ligand and there is no water/ion in pdb/traj files.

Any help/comment will be appreciated.

Bests

Zahra

-----

Upozornení: Není-li v této zpráve výslovne uvedeno jinak, má tato e-mailová zpráva nebo její prílohy pouze informativní charakter. Tato zpráva ani její prílohy v zádném ohledu Biotechnologický ústav AV CR, v. v. i. k nicemu nezavazují. Text této zprávy nebo jejích príloh není návrhem na uzavrení smlouvy, ani prijetím prípadného návrhu na uzavrení smlouvy, ani jiným právním jednáním smerujícím k uzavrení jakékoliv smlouvy a nezakládá predsmluvní odpovednost Biotechnologického ústavu AV CR, v. v. i.

Disclaimer: If not expressly stated otherwise, this e-mail message (including any attached files) is intended purely for informational purposes and does not represent a binding agreement on the part of Institute of Biotechnology CAS. The text of this message and its attachments cannot be considered as a proposal to conclude a contract, nor the acceptance of a proposal to conclude a contract, nor any other legal act leading to concluding any contract, nor does it create any pre-contractual liability on the part of Institute of Biotechnology CAS.