VMD-L Mailing List
From: Shyno Mathew (sm3334_at_columbia.edu)
Date: Mon Nov 23 2015 - 11:10:26 CST
- Next message: Axel Kohlmeyer: "Re: Minimum content/format of PSF file to specify bonds?"
- Previous message: Bret Hess: "Minimum content/format of PSF file to specify bonds?"
- In reply to: Shyno Mathew: "output of salt bridge plugin"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]
Hi all,
Also, how can I include Met, Phe in the salt bridge calculation.
I understand the salt bridge plugin searches for salt bridges between amino
acid residues identified with the VMD keywords acidic and basic, which are
defined in the following way:
atomselect macro acidic "resname ASP GLU"
atomselect macro basic "resname ARG HIS LYS HSP"
So I tried the following:
atomselect macro acidic1 "resname ASP GLU PHE"
atomselect macro basic1 "resname ARG HIS LYS HSP MET"
saltbr -sel [atomselect top "acidic1 or basic1"] -ondist 4 -log SBnew.log
The log file says " found 231 salt bridges". If I don't include PHE, MET I
get 94 salt bridges.
However the individual files are not written and I get the error message:
measure center: bad weight sum, would cause divide by zero
thanks,
Shyno
On Sun, Nov 22, 2015 at 11:40 PM, Shyno Mathew <sm3334_at_columbia.edu> wrote:
> Dear all,
>
>
>
> I have a question regarding the output of salt bridge plugin.
>
>
>
> I understand a salt bridge is considered to be formed if the distance
> between any of the oxygen atoms of acidic residues and the nitrogen atoms
> of basic residues are within the cut-off distance (default 3.2 Angstroms)
> in at least one frame.
>
>
>
> Now when I look at one of my output files, saltbr-ASP19-ARG11.dat,
> following are the values I see:
>
> 0 3.455739012492901
> 1 3.4557396472199486
> 2 3.3294544636949475
> 3 3.2578318095619494
> 4 3.430435352779075
> 5 3.3305625511089834
> 6 4.193335272678875
> 7 3.3836602580806794
> 8 3.7031230566236633
> 9 3.5859244733112283
> 10 3.3892557891669743
>
>
>
>
>
> These values are the average distance between the center of mass of the
> oxygens in the acidic side chain and center of mass of the nitrogens in the
> basic side chain?
>
> In other words, the values in column 2 are not the criteria used to
> identify salt bridges.
>
> Just want to make sure the results indicate there is a salt bridge between ASP19-ARG11
> on all 10 frames although the values are above 3.2 A?
>
>
>
> thanks,
>
> Shyno
>
>
>
>
>
>
> --
> Shyno Mathew
> PhD Candidate
> Department of Chemical Engineering
> Graduate Assistant
> Office of Graduate Student Affairs
> The Fu Foundation School Of Engineering and Applied Science
> Columbia University
>
-- Shyno Mathew PhD Candidate Department of Chemical Engineering Graduate Assistant Office of Graduate Student Affairs The Fu Foundation School Of Engineering and Applied Science Columbia University
- Next message: Axel Kohlmeyer: "Re: Minimum content/format of PSF file to specify bonds?"
- Previous message: Bret Hess: "Minimum content/format of PSF file to specify bonds?"
- In reply to: Shyno Mathew: "output of salt bridge plugin"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]