[AMBER] Problem using charmmlipid2amber.py with VMD

From: <wmsmith.uci.edu>
Date: Fri, 6 Jun 2014 09:27:59 -0700

Hello everyone,
 I am trying to test out the lipid forcefield using AmberTools14. I am
following the tutorial but used VMD to build a POPC membrane.
When I try to run charmmlipid2amber.py:

$ charmmlipid2amber.py -i
'/home/wmsmith/Desktop/Membrane_Sims/Melittin/membrane.pdb' -c
$AMBERHOME/AmberTools/src/etc/charmmlipid2amber/charmmlipid2amber.csv -o

I get the following error:

Traceback (most recent call last):
  File "/usr/local/amber14/bin/charmmlipid2amber.py", line 172, in <module>
    replace_dict[search], line)
KeyError: ' H11 POPC'

After digging through the membrane.pdb and the charrmlipid2amber.csv I
noticed that membrane.pdb contains an H11 atom but this atom is not
included in the csv for POPC type membranes.

Is there a different csv that I need to use when working with membranes
built by VMD?

Thanks in advance,
-Wesley Botello-Smith

AMBER mailing list
Received on Fri Jun 06 2014 - 09:30:02 PDT
Custom Search