Hey All,
I'm having a blast playing with amber thus far!
However, I could use some insight from those who are more experienced.
What I want to do:
create a peptide polymer (minimize it). Then duplicate it and place it's
clone(s) near (not on top) the original. Then create the necessary .prmtop
and inpcrd files so I can play.
What I have tried thus far:
basically followed the B3 tutorial to create the monomer of my choice.
created the prmtop and inpcrd files, minimized and heated up the
structure. used VMD to generate a pdb file.
Here is where things when awry:
used avagadro to duplicate said pdb and rearrange things. saved it as a
pdb file (it runs on open babel). tried to read the pdb file in via xleap
- no good.
realized that I had to add TER statements to separate the chains (no
problem). No good. Got rid of the connection info, didn't help.
I tried reading it into VMD and then saving it, but that didn't work
either. I thought there was an extra letter, that didn't work.
I am getting all kinds of errors regarding:
Nonterminal, was not found in name map
Leap added missing atoms according to residue templates
atoms not in residue templates
I'm confused. I am sure there are a lot of things going on here.
1st - question:
Any recommendations on how to do what i want to do in an easier manner?
(using a differnt gui?)
2nd - question:
Is there something I can do to make the files I already have acceptable to
LEAP?
Thanks,
Jonathan
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Received on Sat Jun 16 2012 - 14:00:03 PDT
