[gmx-users] contact analysis between the all backbone of same protein

[Peter Kroon]

Hi Shahee,


that's a nontrivial question ;)

It depends on what you call a contact; it probably has something to do
with the vdw radius of the CG beads. Either way, we can't answer that
question for you.


Peter

On 19-12-18 10:57, SHAHEE ISLAM wrote:
> hi,
> i am doing the contact between the all backbone beads within a protein
> by using the below command.
> gmx mdmat -f *.trr/xtc -s *.tpr -n index.ndx -mean dm.xpm -t 0.5
> where -t is trunc distance.what value should i use for martini coarse
> grained system because by changing -t value the plots are also
> changes.
> thanking you
> shahee
>
> On 12/19/18, Peter Kroon <p.c.kroon at rug.nl> wrote:
>> Hi Shahee,
>>
>>
>> what cutoff do you mean?
>>
>> You can find sample Martini MDP files here:
>> http://cgmartini.nl/index.php/force-field-parameters/input-parameters.
>>
>> The normal VDW and coulomb cutoffs are 1.1 nm.
>>
>>
>> Peter
>>
>> On 19-12-18 09:30, SHAHEE ISLAM wrote:
>>> thank you so much for your reply.
>>> I have done according your instruction.Can you please tell me what
>>> should best cut off for martini coarse grained force field.
>>>  thanking you
>>> shahee
>>>
>>> On 12/18/18, soumadwip ghosh <soumadwipghosh at gmail.com> wrote:
>>>> Hi,
>>>>
>>>> You can obtain the backbone atom contacts in the same protein using the
>>>> gmx
>>>> mdmat command.
>>>>
>>>> gmx mdmat -f *.trr/xtc -s *.tpr -n index.ndx -mean dm.xpm -t 0.5 (the -t
>>>> option is because you want the protein contacts within 0.5 nm I guess).
>>>> When prompted, select the correct group from index file. It will ask you
>>>> for the group only once.
>>>>
>>>> Then post process the .xpm file into an eps file using,
>>>>
>>>> gmx xpm2ps -f dm.xpm -o dm.eps -rainbow red
>>>> One can view the .eps file in eps viewer and convert it into a .png or
>>>> .tiff file.
>>>>
>>>>
>>>> Best of luck!
>>>>
>>>> Soumadwip Ghosh
>>>> Post Doctoral Research Associate
>>>> Dept of Molecular Imaging & Therapy
>>>> City of Hope National Medical Center
>>>> Duarte, CA - 91010
>>>> United States
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