[gmx-users] Errors during energy minimization of POPC membrane

[Justin Lemkul]

On 10/7/16 11:07 PM, Roshan Shrestha wrote:
> Thanks Justin, but I am not sure how can that be since I downloaded
> the force field from Mackerell Lab, did not show any errors while
> using it for equilibrating my peptide. How can it show errors for my
> bilayer though?
>

Without seeing the topology itself, I can't possibly tell.  But if it came from 
CHARMM-GUI, there's no reason I can think of that it wouldn't work.

-Justin

> On 10/7/16, Roshan Shrestha <roshanpra at gmail.com> wrote:
>> I created a POPC membrane using CHARMM membrane builder, added some water
>> into it using gromacs, did not add any ions since it was already neutral,
>> then I ran its energy minimization using minim.mdp of lysozyme tutorial.
>> However, I ended up with lots of errors like these below after using
>> grompp:
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>> *ERROR 9779 [file topol.top, line 161668]:  No default U-B typesERROR 9780
>> [file topol.top, line 161669]:  No default U-B typesERROR 9781 [file
>> topol.top, line 161671]:  No default U-B typesERROR 9782 [file topol.top,
>> line 161672]:  No default U-B typesERROR 9783 [file topol.top, line
>> 161674]:  No default U-B typesERROR 9784 [file topol.top, line 161675]:  No
>> default U-B typesERROR 9785 [file topol.top, line 161677]:  No default U-B
>> typesERROR 9786 [file topol.top, line 161678]:  No default U-B typesERROR
>> 9787 [file topol.top, line 161680]:  No default U-B typesERROR 9788 [file
>> topol.top, line 161681]:  No default U-B typesExcluding 3 bonded neighbours
>> molecule type 'Other'Excluding 2 bonded neighbours molecule type
>> 'SOL'Removing all charge groups because cutoff-scheme=VerletThere was 1
>> note-------------------------------------------------------Program gmx
>> grompp, VERSION 5.1.3Source code file:
>> /home/roshan/Downloads/gromacs-5.1.3/src/gromacs/gmxpreprocess/grompp.c,
>> line: 1738Fatal error:There were 9788 errors in input file(s)*
>>
>> --
>> Roshan Shrestha
>> Graduate Student
>> Central Department of Physics,Tribhuvan University
>> Kathmandu,Nepal
>>
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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

==================================================