Re: [gmx-users] Re: hydrophobic contacts

[francesco oteri]

Hi,
if you don't want to be very accurate, you can select basing on the residue
name since LEU, ILE, VAL...etc, are universally considered hydrophobic


2012/11/14 Justin Lemkul 

>
>
> On 11/14/12 2:27 AM, Raj wrote:
>
>> Hi all,
>>
>> can some one tel me how can i prepare a index file specifying the
>> hydrophobic atoms along for measuring the hydrophobic contacts in the
>> systems alone.
>>
>>
> There is no straightforward way to do this, as far as I know.  I generally
> construct such groups by selecting groups of hydrophobic residues and then
> parse out the hydrophobic atoms within these groups.  You can narrow down
> your selections using default groups like Sidechain (since the protein
> backbone is highly polar) and select by atom type using a .tpr file as the
> input to make_ndx.
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>
> ==**==
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users
> * Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Searchbefore
>  posting!
> * Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-requ...@gromacs.org.
> * Can't post? Read 
> http://www.gromacs.org/**Support/Mailing_Lists
>



-- 
Cordiali saluti, Dr.Oteri Francesco
-- 
gmx-users mailing listgmx-users@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-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Re: hydrophobic contacts

[Justin Lemkul]

On 11/14/12 2:27 AM, Raj wrote:

Hi all,

can some one tel me how can i prepare a index file specifying the
hydrophobic atoms along for measuring the hydrophobic contacts in the
systems alone.



There is no straightforward way to do this, as far as I know.  I generally 
construct such groups by selecting groups of hydrophobic residues and then parse 
out the hydrophobic atoms within these groups.  You can narrow down your 
selections using default groups like Sidechain (since the protein backbone is 
highly polar) and select by atom type using a .tpr file as the input to make_ndx.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
gmx-users mailing listgmx-users@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-requ...@gromacs.org.

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists