Hi Dan, Thank you for your reply.
I tried what you suggested, and I did get useful information about the residues and atoms that are in contact. However, it seems that the criteria is different than that used with the nativecontacts command, because the number of contacts is much less than the total number of contacts (native and nonnative) calculated with the nativecontacts command. I appreciate your help.
Best regards, Kristin
________________________________________
From: Daniel Roe [daniel.r.roe.gmail.com]
Sent: Friday, March 25, 2016 11:08 AM
To: AMBER Mailing List
Subject: Re: [AMBER] nonnative contacts
Hi,
On Thu, Mar 24, 2016 at 11:27 AM, Krantzman, Kristin D
<KrantzmanK.cofc.edu> wrote:
> Many contacts are formed that are nonnative, but I cannot seem to exact information about the identities of these contacts.
Yes, currently the 'nativecontacts' command is really only set up to
provide detailed information on native contacts. It is presumed that
you have some sort of reference conformation that you want to compare
to. It has been on my ToDo list (if I had a nickel for every time I
said that...) to expand the non-native functionality for a while but I
just haven't gotten to it.
However, I think you can get something like what you want by using the
'hbond' framework. What you need to do is use acceptormask, donormask,
and donorhmask, and then choose no angle cutoff, e.g.
hbond donormask :1-22 donorhmask :1-22 acceptormask :23-1030 dist 3.0
angle -1.0 \
out ncontact.dat avgout avgcontact.dat
What this should do is report all pairs of atoms between :1-22 and
:23-1030 with distance less than 3.0. You specify donorhmask to be the
same as donormask and use no angle cutoff so that cpptraj doesn't
treat these as "normal" hydrogen bonds.
I haven't tested this yet but I think it should work. I'd be
interested to know if/how it works for you. In the meantime I'll start
thinking about getting a better framework for looking at "non-native"
contacts.
Hope this helps,
-Dan
> I will try to explain as best as I can as follows:
> For example, I use the command
> "nativecontacts :1-22 :23-1030 distance 3.0 byresidue resout contactsbyres.dat"
> I get a list of the native contacts by residue and the fraction of frames that the residues are within 3.0.
> When I use the command
> nativecontacts :1-22 :23-1030 distance 3.0 out contacts.dat"
> I get a list of number of native contacts (atoms) and non native contacts (atoms).
> I cannot figure out how I could get an output similar to the contactsbyres.dat, but with both the native and nonnative contacts. Is this possible with cpptraj?
> If not, is there another way for me to determine this?
> Thanks in advance for your help.
> Best, Kristin
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
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Received on Fri Mar 25 2016 - 09:00:04 PDT
