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
membrane_AMB.pdb
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
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Received on Fri Jun 06 2014 - 09:30:02 PDT
