[gmx-users] multiple peptides in the same box

[Mark Abraham]

genconf has other modes that may be useful here.

Mark
On Apr 12, 2014 3:59 AM, "Justin Lemkul" <jalemkul at vt.edu> wrote:

>
>
> On 4/11/14, 9:29 PM, maggin wrote:
>
>> Hi, Justin
>>
>> Thank you very much!
>>
>> If I want 6 peptides in a same box, I revised it as follow:
>>
>> 1.pdb2gmx -f 1IYT.pdb -o 1IYT.gro -ignh -ter -water  spce  -p 1IYT.top
>>
>> 2.genconf -f 1IYT.gro -nbox 1 1 1  -o 1IYTlarge_box.gro -renumber -rot
>> -maxrot 180 180 180
>>
>> 3.editconf -f 1IYTlarge_box.gro -o 1IYT_newbox.gro -c -d 1 -bt cubic
>>
>> 4.genbox -cp 1IYT_newbox.gro -nmol 5  -ci 1IYT.gro -p 1IYT.top  -o
>> 1IYT_6.gro -try 500
>>
>> However, when I use VMD to check the 1IYT_6.gro, and get 12 fragments(12
>> proteins), actually I should get 6 fragments.
>> <http://gromacs.5086.x6.nabble.com/file/n5015805/A_
>> 4SO89OF207_N%29J7%60P%5DD3J.jpg>
>>
>> <http://gromacs.5086.x6.nabble.com/file/n5015805/_AQUOZ%6042UMR8%60%24L9%
>> 7BFKDD8.jpg>
>>
>> How I fix it? Thank you very much!
>>
>>
> Either the molecules are split across periodic boundaries (which VMD knows
> nothing about, so it thinks the protein segments are separate), or the use
> of genbox -ci -nmol has inserted fragments of molecules.  You can easily
> check by noting the number of atoms in the coordinate file.  If it is
> exactly 6 times a single peptide, then it's just a PBC thing.  It's
> entirely possible that genbox fragmented the molecules; the use of -ci
> -nmol is not designed for multi-residue molecules.  If it works, great, if
> not, you'll need to come up with another way to prepare the system.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> 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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