use -chainsep interactive option in pdb2gmx.
Suman
On Wed, 11 Jan 2012 16:42:12 +0530 wrote
>Dear all:
I want to do a simulation using a dimer, but the system is connected by 2
disulfide bonds between A-chain and B-chain. I have produced topology file for
protein with pdb2gmx using AMBER99SB forcefield. In order to bond disulfide
bonds I using flag -ss. If I do not delete the TER line between A-chain and
B-chain in .pdb file, the program pdb2gmx can not recognize the disulfide bonds
between A-chain and B-chain. But if I delete the TER line, I get the two bonds
successfully. There would be another problem, the C-terminal of A-chain and the
N-terminal will be bonded in the .top file. How should I do?
I am using gromacs 4.5.4!
Sincerely yours,
Xianwei Wang
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Suman Kumar Nandy
Senior Research Fellow
Department of Biochemistry & Biophysics
University of Kalyani
Kalyani-741235
India.
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
