[gmx-users] conversion of gromacs files to amber files

[Oliver Grant]

Hi Leila,

I would try the other suggested options like catdcd or vmd. The script is a
pain and you would have to adapt it to work with DNA. It cost me a lot of
time.

I used g_hbond for residence time like this:

g_hbond -f 8_fullMD_CA.xtc -s 7_fullMD.tpr -n g_hbond.ndx -a 170 -num >
g_hbond.log   //the tpr file can't have restraints in it for some reason,
thats why it is 7 and not 8.
// ndx file has the 3 atoms in the hbond

Checking for overlap in atoms between 0SA and SER
Calculating hydrogen bonds between 0SA (1 atoms) and SER (2 atoms)
Found 1 donors and 2 acceptors

Will do grid-seach on 16x16x16 grid, rcut=0.35
Average number of hbonds per timeframe 0.872 out of 1 possible  // so here's
the % residence

I found which residues were involved in hbonding to my ligand with an
initial g_hbond run. I think you can get all the info you need from g_hbond.

Oliver


On 7 December 2010 11:37, leila karami <karami.leila1 at gmail.com> wrote:

> Dear Oliver
>
> very thanks for your help.
>
> Justin's perl script is good for direct hydrogen bonds, while I want to
> study water
> mediated hydrogen bonds and residence time and occupation of them.
>
> Are youe sure g_hbond give you residence time of hydrogen bonds?
>
> before you said you used a script to change the pdb file for compatibility
> with amber.
>
> please share me that.
>
> --
>
>
> Leila Karami
> Ph.D. student of Physical Chemistry
>
> K.N. Toosi University of Technology
> Theoretical Physical Chemistry Group
>
>
>
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20101207/151d8b30/attachment.html>