It's working now :) Thank you Dan.
-Sook Wong
-----Original Message-----
From: Wong, Sook (NIH/NCATS) [V]
Sent: Thursday, April 02, 2015 3:52 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Lipid Conversion from Charmm PDB to Lipid14 PDB
Dan,
I have the following after removing of "\":
$ charmmlipid2amber.py -i step5_assembly.pdb -c $AMBERHOME/AmberTools/src/etc/charmmlipid2amber/charmmlipid2amber.csv -o step5.pdb
Error: No residues substituted
Any advice,
Sook Wong
-----Original Message-----
From: Daniel Roe [mailto:daniel.r.roe.gmail.com]
Sent: Thursday, April 02, 2015 3:40 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Lipid Conversion from Charmm PDB to Lipid14 PDB
Hi,
On Thu, Apr 2, 2015 at 1:35 PM, Wong, Sook (NIH/NCATS) [V] <sook.wong.nih.gov> wrote:
> Hi,
>
> I am facing an issue on converting the DPPC membrane PDB from charmm to lipid14 using charmmlipid2amber. Ended up with the following:
>
> [****]$ charmmlipid2amber.py -i step5_assembly.pdb \ -c
> path/AmberTools/src/etc/charmmlipid2amber/charmmlipid2amber.csv \ -o
> step5.pdb
> Usage: charmmlipid2amber.py [-c charmmlipid2amber.csv] -i input.pdb -o
> output.pdb
What happens if you remove the backslash characters ('\') when you enter the command?
-Dan
>
> There is no output pdb generated from the command and I am not sure why. Appreciate if anyone can help.
>
> -Sook
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Thu Apr 02 2015 - 13:00:07 PDT
