Lin,
Gromacs isn't choosing a specific condition, but rather it building
the protein using a set of defaults. Try looking at the documentation
for pdb2gmx, which clearly states the defaults that the program uses
for assigning the protonation state of the residues of interest.
Given those defaults, you need to decide if they are appropriate for
the conditions you are trying to simulate, and if not, you need to
change them accordingly.
Josh
On May 24, 2009, at 11:37 PM, Chih-Ying Lin wrote:
Hi
I am a bit confused.
1LW9.pdb = T4 lysozyme
After this command,
pdb2gmx -f 1LW9.pdb -o 1LW9.gro -p 1LW9.top
=> GG 45a3 is choosed.
The Gromacs tells me that it carries +8 charges.
As we know, that the amount of charges which the protein carries is
based on pH values. So, my question is
this command =>
pdb2gmx -f 1LW9.pdb -o 1LW9.gro -p 1LW9.top
at what condition Gromacs calculate the charges of the protein??
Thank you
Lin
Chih-Ying Lin wrote:
Hi
after the command pdb2gmx,
the protein will be added appropriate H,
So, does pdb2gmx add H (protonate) based on pH =7.0 ?
No. You should choose the protonation state based on your
understanding
of the conditions you wish to model, and instruct pdb2gmx accordingly.
Read pdb2gmx -h. Do some tutorials - this sort of thing is covered
there.
Mark
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Joshua L. Adelman
Biophysics Graduate Group Lab: 510.643.2159
218 Wellman Hall Fax: 510.642.7428
University of California, Berkeley http://nature.berkeley.edu/
~jadelman
Berkeley, CA 94720 USA jadel...@berkeley.edu
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