I have another question about the option -ter of the pdb2gmx command. I choose it because I thought that this is a way that I can determine what shell happen with the termini but I was not ask anything by the program.
My aim is it to block the termini with a neutral group. Is there a way to do this with gromacs? Best, Eva > Hi Justin, > thank you for your mail. > Sorry that I didn't first check than help. > Eva > >> >> >> On 7/11/12 10:24 AM, [email protected] wrote: >>> Hi everybody, >>> >>> I wanted to ask if there is a possibility to tell pdb2gmx which >>> residues >>> I >>> want to be protonated or not. >>> So that I can for example say HIS at position 29 shell be protonated >>> twice. >>> >>> I need this for further electrostatic analysis. >>> >> >> Please read pdb2gmx -h. There are tons of available options to control >> protonation of any and all titratable residues. >> >> -Justin >> >> -- >> ======================================== >> >> Justin A. Lemkul, Ph.D. >> Research Scientist >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu | (540) 231-9080 >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> >> >> -- >> gmx-users mailing list [email protected] >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> * Only plain text messages are allowed! >> * 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 >> > > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Only plain text messages are allowed! > * 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 > -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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
