Hi,
On Thu, Apr 7, 2016 at 8:49 AM, Krantzman, Kristin D
<KrantzmanK.cofc.edu> wrote:
> 1. The number of contacts calculated with the above hbond command at frame 1 is 20. When I use the nativecontacts command (nativecontacts :1-22 :23-1030 distance 3.0 out contacts.dat), the number of native contacts in frame 1 is 61. Why are the number of contacts calculated with these two commands so different when the same distance criterion is used?
First, one minor point; you are using slightly different distance
cutoffs in each command (3.05 vs 3.0). That said, there are two other
reasons the results are different.
The first is that by default distances in the 'hbond' command are not
imaged, while those in the 'nativecontacts' command are. So either use
the 'image' keyword with 'hbond' or the 'noimage' keyword with
nativecontacts; note that imaging will make the calculation slower but
will capture interactions that occur across periodic boundaries.
The second is that due to the way the 'hbond' command is coded, it
currently skips all non-H atoms in 'donormask'. This makes sense for
hydrogen bonds but means that 'donormask' in 'hbond' is not selecting
any H atoms. To ensure that the masks are selecting the same atoms in
each command add '&!.H=' (and not atoms starting with H) to all of
your masks, e.g. ':1-22&!.H=' and so on.
> 2. I do not completely understand the significance of the third atom (DonorH) that is in the avgcontact.dat file.
> In the avgcontact.dat file, I have three columns of atoms, Acceptor, DonorH and Donor. Is the distance measured between the atom in the Acceptor column and the atom in the Donor column? What is the importance of the third atom in the DonorH column? How is this particular atom selected?
Cpptraj defines hydrogen bonds as being between a donor heavy atom,
donor hydrogen, and acceptor heavy atom (D-H -- A); the distance
cutoff is the distance between D and A, while the angle cutoff refers
to the angle between D, H, and A. The Amber15 manual actually has a
pretty good explanation of how all of this works (section 29.9.25
hbond).
-Dan
>
> I appreciate your help with all of this.
> If you could clarify the difference between the calculations with these two different commands, this would be useful.
>
> If you have other ideas about how I could obtain this information, that would be helpful. I am pretty adept at writing code in Fortran 90 and scripts in Perl.
>
> Thanks for all of your help.
>
> Best, 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
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
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>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Thu Apr 07 2016 - 09:00:03 PDT
