[gmx-users] Issues combining protein and membrane file?
Sanim Rahman
sanimr at mail.usf.edu
Sun Feb 19 01:34:58 CET 2017
My apologies, I sent you the wrong file. Here is the right one. I made the
edits and all the atoms are properly accounted for in VMD but they are not
visible. Also when I used the inflategro script on it, only 148 atoms were
read. Here is the command I used:
perl inflategro.pl system.gro 4 POPC 14 system_inflated.gro 5 area.dat
Here are the files I attached:
Original- https://www.dropbox.com/s/aaj4q4efrjxmj3b/system.gro?dl=0
Inflated- https://www.dropbox.com/s/aiu89i1n5nj5bpp/system_inflated.gro?dl=0
Regards,
Sanim Rahman
On Sat, Feb 18, 2017 at 7:22 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 2/18/17 6:55 PM, Sanim Rahman wrote:
>
>> 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
>>
>>
> The file needs a title line. The number of atoms must be the second line,
> not the first.
>
> http://manual.gromacs.org/documentation/2016.2/user-guide/fi
> le-formats.html#gro
>
> -Justin
>
>
> 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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> --
> ==================================================
>
> 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
>
> ==================================================
> --
> Gromacs Users mailing list
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