On Mon, Sep 07, 2020, Sarah Jane wrote:
>> HAR = sequence {ACE HAR NME}
Again, don't reuse the idenifier "HAR". Just type something like:
x = sequence {ACE HAR NME}
Now the simplest thing to do is to use the bond command to add any
missing bonds. If you are going to be using the HAR residue a lot, you
could use tleap to set the connect0 and connect1 atoms to the N and C
atoms of the HAR residue (then use saveOff to save this as an off file
for use later.) But try the simpler thing first.
After you create a prmtop file, use parmed to ensure that you have the
bonds you want.
....dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Sep 07 2020 - 09:00:05 PDT
