Turgay Cakmak wrote:
Hi gromacs users,
I have two different molecules, lets say A and B. I want to put 5 A
molecules and 5 B molecules in the same box.
I carried out the following steps.
1) For both A and B, I used *genbox* with *-nmol* flag separetely
and obtained the A_multiple and the B_multiple structure files.
2) Using *cat* command, I concatanated two structure files
(A_multiple, B_multiple) to get system.gro.
3) Using the *pdb2gmx*, I got conf.gro and topol.top of system..
But, I am not sure if this is the correct way? Because, when I look the
conf.gro at VMD, I saw that some part of the A molecule and B molecule
had overlapped.
Could anybody help me please?
An alternate procedure:
1. Run pdb2gmx on a single molecule of A and a single molecule of B
2. Convert the two resulting .top files into .itp files (see the manual or wiki
for the differences) and construct a simple .top that #includes these
3. Build your system for molecule A as you did before
4. Insert 5 molecules of B into the A system to avoid clashes
This way you avoid a lot of topological redundancy and eliminate clashes.
-Justin
Turgay
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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