[gmx-users] Issues combining protein and membrane file?
Justin Lemkul
jalemkul at vt.edu
Sun Feb 19 01:38:18 CET 2017
On 2/18/17 7:34 PM, Sanim Rahman wrote:
> 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
The number of atoms is wrong (note that VMD prints out an error message to this
effect, you have 80188 atoms, not 80189) and your columns are misaligned
starting with the lipids, so the content of the file is unintelligible. The
.gro file format has a fixed format (see link posted previously) and all
programs that read them expect that format.
-Justin
> 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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>>>> Gromacs Users mailing list
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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
>>
>> ==================================================
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>> Gromacs Users mailing list
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>> * Please search the archive at http://www.gromacs.org/Support
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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
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