[gmx-users] merging chains in gromos43a1p

[Justin Lemkul]

On 12/8/14 6:21 PM, Jayant James wrote:
> Hi!
> In continuation with the thread that GMX version 4.5.4 is not able to merge
> files. I thought that I should include the error message for more clarity
> so that you can see that error and suggest if I really need the latest
> version of GMX installed.
> So do you really think that installing the latest version of GMX would
> solve the problem?

Yes.

-Justin

> Thanks
> James
>
> -------------------------------------------------------
> Program pdb2gmx, VERSION 4.5.4
> Source code file: statutil.c, line: 819
> Invalid command line argument:
> -merge
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
>
> On Wed, Dec 3, 2014 at 2:55 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 12/3/14 4:52 PM, Jayant James wrote:
>>
>>> Hi!
>>> I was wondering if there is the -merge option in pdb2gmx in gromacs 4.5.4?
>>> It some how seems like version 4.5.4 that I have for simulating
>>> phosphorylated serines does not have this option.
>>> Since I am trying to simulate a protein that has three chains comprised
>>> into one protein I normally prefer to number them sequentially. The
>>> sequential numbering helps in indexing for simulated annealing because it
>>> is easy to choose the amino acids that I need to heat and cool.
>>>
>>
>> My 43a1p files work with any version from 4.5 onward, so you can (and
>> probably should) use a newer Gromacs version.  The "version 4.5" tag just
>> indicates that's when the organization of the files changed.
>>
>> -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

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