Re: [AMBER] nativecontacts

From: Abelak, Kavin <>
Date: Mon, 23 May 2016 09:40:02 +0000

Hi Neha,

As I understand it, if there is more than one native contact between residue pairs (i.e., contacts between more than one atom pair) you will likely get fractions > 1. See p583 of the AmberTools15 manual.


On 23 May 2016, at 08:25, Neha Gandhi <<>> wrote:

I have 60000 frames in total and I am using following command to calculate
contacts (AMBER14 and ambertools15). WIth Ambertools16, it prints fraction
as 0 with the same command.

nativecontacts :LIG !:POP writecontacts contacts.out resout resout.out
distance 10 includesolvent byresidue map mapout resmap.gnu series seriesout
sout.out reference

For some residues I can contact fraction > 100. Is it really possible.e.g.
output below

#Res1 #Res2 TotalFrac Contacts
442 206 582.479 813

Am I doing this correctly?

Dr. Neha S. Gandhi,
Vice Chancellor's Research Fellow,
Queensland University of Technology,
2 George Street, Brisbane, QLD 4000
Research Gate
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Received on Mon May 23 2016 - 03:00:02 PDT
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