[gmx-users] merging chains in gromos43a1p

[Jayant James]

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?
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.
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>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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-- 
Jayasundar Jayant James

http://www.chick.com/reading/tracts/0076/0076_01.asp