[gmx-users] Re: Connecting sidechains in gromacs file

Thanks Baofu. It seems that my topology file indeed is missing bonds for the sidechains! I am using a webtool so I am wondering whether the tool does not support these residues. > are you sure that your topology file is correctly written? On 07/15/2011 11:34 AM, Zack Scholl wrote: >

[gmx-users] Connecting sidechains in gromacs file

hanks, Sincerely, Zack Scholl -- gmx-users mailing listgmx-users@gromacs.org 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 in

[gmx-users] Re: Relaxed frozen groups

>>Zack Scholl wrote: >> Hi all- >> >> Is it possible to freeze a group of atoms only partially in a >> direction? For instance, could I freeze a group inside a box of a >> definite size? >> >> > Not by defining a box, as such, but you can free

[gmx-users] Relaxed frozen groups

Hi all- Is it possible to freeze a group of atoms only partially in a direction? For instance, could I freeze a group inside a box of a definite size? Sincere thanks, Zack -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the

[gmx-users] Programs to add residues

Hi all, Is there a program that allows the user to add residues to the N and C terminus, without using the electron density? I would like to add a short linker to my protein which doesn't exist in the electron density. Thanks a lot, Sincerely, Zack -- gmx-users mailing listgmx-users@gromac

[gmx-users] Combining part files after using -noappend

Hi all, I just discovered nohup for running my simulation without hangup. For some reason using nohup wouldn't except the checksum on my previous md.log file so I just added the -noappend option to create new files. I'm curious, is there a way to combine the part files that emerge from using the