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
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
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
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
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