Re: [AMBER] nativecontacts command in CPPTRAJ

From: Andreas Tosstorff <>
Date: Sun, 6 May 2018 14:05:41 +0200

Hey Ruth,
maybe the non-native option of the command is what you are looking for?


> Am 06.05.2018 um 12:31 schrieb Ruth Helena Tichauer <>:
> Dear Amber users and developers,
> I’ve run QM/MM simulations of a protein with its ligand.
> While visualising the obtained trajectories, I’ve 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 I’m 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,
> Ruth
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Received on Sun May 06 2018 - 05:30:08 PDT
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