[gmx-users] Re: Requesting Help

[XAvier Periole]

Anirban,

It is better to keep conversations on the gmx-user list where I
believe you found much help already.

I looked quickly at your EM.gro file. There several issues that
you should have picked your self quite easily using VMD.

1- there are 3 empty line in your gro file: lines 204, 2253 and 4302.

2- when this fixed and the number of atoms in the second line of
the file changed, I looked at the protein only and noticed very clearly
that your conformation, although looking reasonable overall, has
serious problems. This is clear when looking at the backbone
only. Several portions of your protein have Calpha-Calpha distances
that exceed a reasonable distance (0.42 nm). Note that in the MARTINI
2.1 version the distance is 0.35 nm.
You can visualize them by uploading your corrected EM.gro in VMD
and choosing a "dynamicbonds" representation on the following selected
atoms:
name "BC*.*" "BH*.*", the missing atoms would appear by repeating
this selection and showing them in CPK.

I picked the following regions but it might be more:
- residues 33-38
- 105-108
- 141-161 (this one is really funky)
- 168-171
- 200-206
- 212-213
- 239-246
- 253-258

This is only where distances appear too long but all over the structure
distances also appeared to short.

In conclusion your protein structure is seriously damaged, this is  
probably
not a problem of your protocol but your atomistic starting structure.  
You
should check it and fix it before going further in the simulation.

This should help.
XAvier.


On Nov 3, 2009, at 6:16 AM, Anirban wrote:

> Respected Sir,
>
> Thank you very much for the reply.
> Actually, packed the lipids around my protein using InflateGRO program
> and then solvated it using genbox. Then I ran EM which ran quite well.
> But still am getting that error. I am attaching my .gro file. If you
> find any time, please have a look at it and comment.
> Thank you once again.
>
> Regards,
>
>
>
> On Sat, 2009-10-31 at 10:49 +0100, XAvier Periole wrote:
>> Dear Anirban,
>>
>> Your mdp file seems fine to me.
>> If I were you I would look at the system. It probably contains bad
>> contacts between different parts you put together, which makes
>> it explode, if this is what happens (difficult to tell from the  
>> output
>> message).
>>
>> I would also suggest that you contact the gmx-user list and search
>> the archive. Someone might have had the same problem or might
>> be able to help you.
>>
>> Best,
>> XAvier.
>>
>> On Oct 30, 2009, at 4:13 PM, Anirban wrote:
>>
>>> Respected Sir,
>>>
>>> I have gone through your paper on Rhodopsin self-assembly study.
>>> I am also trying a similar thing on the CGMD study of a GPCR protein
>>> in
>>> a lipid bilayer. I have using MARTINI FF and have successfully built
>>> my
>>> system. The EM ran well, but I am getting problem with MD run. I am
>>> attaching my mdp file. I am getting the following error in the very
>>> first step:
>>>
>>> Number of grid cells is zero. Probably the system and box collapsed.
>>>
>>> Please advice how to solve this issue.
>>>
>>> Regards,
>>>
>>>
>>> -- 
>>> Anirban Ghosh
>>> Grade Based Engineer
>>> Bioinformatics Team
>>> Scientific & Engineering Computing Group
>>> Centre for Development of Advanced Computing
>>> Pune, India
>>>
>>> -- 
>>> This message has been scanned for viruses and
>>> dangerous content by MailScanner, and is
>>> believed to be clean.
>>>
>>> <md.mdp>
>>
>>
> -- 
> Anirban Ghosh
> Grade Based Engineer
> Bioinformatics Team
> Scientific & Engineering Computing Group
> Centre for Development of Advanced Computing
> Pune, India
>
> -- 
> This message has been scanned for viruses and
> dangerous content by MailScanner, and is
> believed to be clean.
>
> <EM.gro>