[gmx-users] AMBER and gromacs atoms renaming

Hi, I am running a simulation of a protein DNA complex, and for this i am using AMBER99 forcefield. The problem is that every complex I need to run, I have to rename several residues and atoms, especially hydrogen atoms one by one (well, actually using replace tool). And this takes hours to get don

Re: [gmx-users] AMBER and gromacs atoms renaming

Ragnarok sdf wrote: Hi, I am running a simulation of a protein DNA complex, and for this i am using AMBER99 forcefield. The problem is that every complex I need to run, I have to rename several residues and atoms, especially hydrogen atoms one by one (well, actually using replace tool). And thi

RE: [gmx-users] AMBER and gromacs atoms renaming

Can this help? http://www.gromacs.org/pipermail/gmx-users/2006-March/020599.html I found using the users-gmx mailing list archives (you should search the archive before posting): http://www.gromacs.org/component/option,com_wrapper/Itemid,165/ If that doesn't solve your problem, you can always writ

Re: [gmx-users] AMBER and gromacs atoms renaming

Hi, Well, sed's a good friend to have in these cases :) e.g. converting lysine residue names: sed -e 's/LYSH/LYP /' -e 's/LYS/LYN/' gromacs.pdb > amber.pdb or converting the C7 of thymine to C5M: sed -e 's/\(^.\{13\}C\)7 THY/\15M THY/' gromacs.pdb > amber.pdb Note that this can be easily exten