[gmx-users] multiple peptides in the same box

[Justin Lemkul]

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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