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 _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
