Dear all,
I want to run some simulations of a kinase with an ATP molecule using
gromacs 4.5.1 with the gromos53a6.ff forcefield. To generate the .gro and
.top files I am running
pdb2gmx -v -f ATP.pdb -p initial.top -o initial.gro -ff gromos53a6 -water spc
Now the generated topology file shows so
Dear Tom,
I know that there were some ATP-related issues in past versions of gromacs
using the gromos-ff: Gromos used some 5-letter atom types which was a
problem as the pdb file format only has 4 columns for them so you had to
do some renaming. I thought this not to be an issue anymore and am
sur
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