Re: [AMBER] Problem using with VMD

From: Benjamin D Madej <>
Date: Mon, 9 Jun 2014 19:18:57 +0000

Hi James and Wesley,

Yes, I'm still ironing out a couple of bugs. If you're having trouble with the residue numbering please download the fixed script available here:

As far as I know, our scripts are the only available that can reorder atoms and residues in a PDB properly for LEaP and Lipid14. The closest thing that I could find that has similar functionality is the biopython PDB tools.

As for the VMD builder: Build the POPC bilayer with the "c36" force field set and then convert with There is significantly different atom naming with the POPC c27 force field, as you found. I'll look into possibly adding a file for c27 CHARMM lipids.

It's also quite straightforward to copy the charmmlipid2amber.csv file and create your own substitutions, if necessary. I can explain it if anyone's interested.

All the best,
Ben Madej
UCSD Chemistry and Biochemistry

From: James Starlight []
Sent: Sunday, June 08, 2014 12:52 AM
To: AMBER Mailing List
Subject: Re: [AMBER] Problem using with VMD

Hi Wesley,

I had the same problems with this python script. As Ross Walker said
during amber workshop this sript could contain some bugs which will be
fixed. Does anybody knows some other script for conversion of the charm-gui
membranes to the amber pdb's?


2014-06-06 18:27 GMT+02:00 <>:

> 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
> $ -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/", 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 Mon Jun 09 2014 - 12:30:04 PDT
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