[gmx-users] Simulation of membrane protein in vacuu

[James Starlight]

Dear Gromacs users!


I want to simulate membrane receptor in the Gromos 56 force field in the
vacuu and I have some methodological questions.


1- I need to edit topology of my structure by adding one DOUBLE covalent
bond between desires atoms ( they have been already placed in the desired
adjacent positions by pymol).

I add string in topology.top [bonds]

 2809  2810     2    gb_5

Does it enough? What addition modification of the topology file requires
for the addition covalent bond?

Where I could found names of all bonds parametrs such as gb_5 ?
I've found that number for the C=O pair so as I understood this must
correspond to double planar bond.

2- I've received message that my system consist of 2 negative charges. For
water-souluble proteins I just place 2 counter ions in the SOLVENT to
neitralize this charge. What I should do for the vacuu simulation ?


Thanks!

James
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