Hi Thomas,
You could adapt the charmmlipid2amber.py to go the reverse direction. The trick is that you'd have to pre-process the PDB structure file so that the three "residues" in each lipid have the same residue number. Then you could create a custom substitution file for that type of residue and run the script again.
Take a look at the substitution file. It has a fairly straightforward format:
residue,order,search,replace,TER,num_atom
residue: residue name
order: atom order in residue
search: search string for PDB file columns 13-21
replace: replace string for PDB file columns 13-21
TER: if True, add a TER card at the end of the residue
num_atom: number of atoms in residue
All the best,
Ben Madej
UCSD Chemistry and Biochemistry
SDSC
________________________________________
From: Thomas Evangelidis [tevang3.gmail.com]
Sent: Monday, June 09, 2014 12:48 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Problem using charmmlipid2amber.py with VMD
Hello Ben,
I am interested in the opposite direction, namely amber->charmmlipid for a
POPE bilayer. Is there any script that can do this? If not, could you
please give me some extra details about how to do these substitutions using
the charmmlipid2amber.csv file?
thanks,
Thomas
On 9 June 2014 22:18, Benjamin D Madej <bmadej.ucsd.edu> wrote:
> 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:
> https://dl.dropboxusercontent.com/u/26203202/charmmlipid2amber.tar.bz2
>
> 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 charmmlipid2amber.py. 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
> SDSC
>
> ________________________________________
> From: James Starlight [jmsstarlight.gmail.com]
> Sent: Sunday, June 08, 2014 12:52 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] Problem using charmmlipid2amber.py 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?
>
> James
>
>
> 2014-06-06 18:27 GMT+02:00 <wmsmith.uci.edu>:
>
> > 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
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
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>
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>
--
======================================================================
Thomas Evangelidis
PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
Panepistimioupoli-Zografou
157 71 Athens
GREECE
email: tevang.pharm.uoa.gr
tevang3.gmail.com
website: https://sites.google.com/site/thomasevangelidishomepage/
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Received on Mon Jun 09 2014 - 17:30:02 PDT
