[gmx-users] multiple peptides in the same box

[maggin]

Hi, everyone

I want to put 12 peptides randomly in position and orientation in the same
box. I'm not sure if the following is right, so I asked for help, please
check if something wrong in it? Thank you very much for your kind help and
suggestion !

1. pdb2gmx -f 1IYT.pdb -o 1IYT.gro -ignh -ter -water  spce  -ss  -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
-density 1000 -rotate 60 60 60

4. genbox -cp 1IYT_newbox.gro -nmol 11  -ci 1IYT_newbox.gro  -p topol.top
-cs spc216.gro -o 1IYT_solv.gro 

At here, after delet  the #include "ffgromos43a1.itp" line, as well as all
lines after the #endif line in the position restraint section. This includes
any lines referring to spce.itp and ions.itp, as well as the [ system ] and
[ molecules ] directives.

I creat the top file, the content topol.top as follows:

; GROMACS topology
;
; Include the force field
#include "gromos43a1.itp"

; Include chain topologies
#include "topol_A.itp"
#include "topol_B.itp"
#include "topol_C.itp"
#include "topol_D.itp"
#include "topol_E.itp"
#include "topol_F.itp"
#include "topol_G.itp"
#include "topol_H.itp"
#include "topol_I.itp"
#include "topol_J.itp"
#include "topol_K.itp"
#include "topol_L.itp"

; Include water topology
#include "spce.itp"

; Include generic ion topology
#include "ions.itp"

[ system ]
Twelve proteins in water

[ molecules ]
Protein_A	1
Protein_B	1
Protein_C	1
Protein_D	1
Protein_E	1
Protein_F	1
Protein_G	1
Protein_H	1
Protein_I	1
Protein_J	1
Protein_K	1
Protein_L	1


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