[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 <jalemkul at vt.edu>

>
>
> 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
>
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> ==============================**==========
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> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
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-- 
Cordiali saluti, Dr.Oteri Francesco