Re: [AMBER] nativecontacts command in CPPTRAJ

From: Sowmya Indrakumar <>
Date: Sun, 6 May 2018 15:13:32 +0000

Hey Ruth,

You may want to try this, this works fine for me:

parm file.parm7


strip :WAT #optional
reference min.rst7
nativecontacts :179&!.CA,C,O,N,H writecontacts nativecontacts.dat resout res noimage distance 8.0 out contacts.out first resoffset 4 contactpdb contacts.pdb byresidue map mapout gnu series seriesout nativeseries.dat


From: Ruth Helena Tichauer <>
Sent: Sunday, May 6, 2018 12:31:06 PM
To: AMBER Mailing List
Subject: [AMBER] nativecontacts command in CPPTRAJ

Dear Amber users and developers,

Iíve run QM/MM simulations of a protein with its ligand.

While visualising the obtained trajectories, Iíve noticed that a given residue (179) engages in different interactions in the initial structure and during the production phase. To depict this structural rearrangements, I wanted to use the nativecontacts command from CPPTRAJ in a manner that it would calculate the by residue native contacts present in the initial structure, given as a reference, and then show that these native contacts are lost and others are formed (non native contacts become native contacts) using the following input file:

#Load topology and trajectories
parm ../native2.parm
trajin ../
reference ../../../2/Neutralized/nat2_md-qm_0.pdb parm ../native2.parm

#Native contacts analysis
nativecontacts :179&!.CA,C,O,N,H \
byresidue resoffset 4 out nat2-0_NC-179.nb \
noimage distance 8.0 reference \
writecontacts nat2-0_NC-179.out \
resout nat2-0_NC-179.resout \
series seriesout nat2-0_NC-179.nc_vs_t \
map mapout nat2-0_NC-179 \

Nevertheless I get empty files.. As it is the first time Iím using this command, I suspect there are some errors in it, please help me correct it in order to get the information I wish (native contacts vs time, non native contacts vs time, strength of contacts made, lasting native contacts..).

Thank you in advance,

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Received on Sun May 06 2018 - 08:30:02 PDT
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