[gmx-users] Issues combining protein and membrane file?

[Sanim Rahman]

Thank you Justin,

I was able to remove the velocities from my file but it still fails to
read. I attached a dropbox link to my file if you have the time to take a
look at it.

https://www.dropbox.com/s/aaj4q4efrjxmj3b/system.gro?dl=0

Thank you!

Regards,
Sanim Rahman


On Sat, Feb 18, 2017 at 5:18 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 2/18/17 4:46 PM, Sanim Rahman wrote:
>
>> Hi all,
>>
>> I am trying to prepare a system for a MD simulation of an ion channel
>> (Kv1.2) in a POPC lipid bilayer. I am struggling inserting the protein
>> into
>> the lipid membrane. I am currently trying the inflategro.pl approach done
>> in the KALP15 tutorial. The first step with the prepared structural files
>> was to combine them together using
>>
>> cat protein.gro lipid.gro > system.gro
>>
>> However, after combining them and loading them into VMD, my system has
>> become distorted and only 151 atoms out 90131 atoms were read. Is there
>> anything I can do to fix this issue?
>>
>> I believe it may have to do with the nomenclature of my script. The .gro
>> file for my protein and lipid bilayer is not written in a consistent
>> format:
>>
>>   421THR     CA10936   4.791   7.926   7.910
>>   421THR     CB10937   4.822   7.797   7.831
>>   421THR    OG110938   4.862   7.831   7.698
>>   421THR    HG110939   4.882   7.748   7.647
>>   421THR    CG210940   4.701   7.705   7.826
>>   421THR      C10941   4.754   7.892   8.055
>>   421THR     O110942   4.772   7.974   8.146
>>   421THR     O210943   4.649   7.808   8.074
>>     1POPC    C1    1   5.168   4.220   4.016 -0.2491  0.0715  0.4836
>>     1POPC    C2    2   4.942   4.276   3.936  0.1967  0.1087 -0.5850
>>     1POPC    C3    3   5.108   4.444   3.993  0.3211  0.0553 -0.2150
>>     1POPC    N4    4   5.085   4.311   3.935  0.2251  0.0126 -0.0777
>>     1POPC    C5    5   5.129   4.301   3.795 -0.0894 -0.4945 -0.1460
>>     1POPC    C6    6   5.280   4.304   3.767  0.0019 -0.2403  0.3568
>>     1POPC   OS7    7   5.354   4.422   3.799  0.0579 -0.0618 -0.4147
>>     1POPC    P8    8   5.512   4.403   3.778  0.1576  0.2198  0.0575
>>     1POPC   OM9    9   5.532   4.289   3.686  0.1757 -0.1049  0.4662
>>     1POPC  OM10   10   5.597   4.524   3.785  0.1671  0.2024  0.2449
>>     1POPC  OS11   11   5.526   4.331   3.921  0.4792 -0.0093 -0.0879
>>
>>
> VMD is probably choking on the fact that some of your lines have velocity
> information (the lipids) and others (the protein) don't.  Try stripping the
> velocities and appending just the coordinates.
>
> I updated the number of atoms in my system and removed nonessential lines
>> as well. Also, would the inflategro procedure be appropriate for this
>> simulation considering that I am inserting a +10,000 atom protein into a
>> lipid membrane?
>>
>>
> Sure, we've done it with big systems, though the script is a bit of a
> memory hog, IIRC.  Haven't used it in a while.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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