Dear Amber List members,
I have been studying on my Ubuntu linux workstation
the Amber14 tutorial A16
An Amber Lipid Force Field Tutorial: Lipid14
<
http://ambermd.org/tutorials/advanced/tutorial16/index.html>
By Ben Madej & Ross Walker.
I have built using Charmm-Gui the protein-in-membrane complex
as step5_assembly.pdb file,
where following the tutorial directions I added
a TER card after the protein chain. I cannot attach the pdb file -
it is too big, so moderator denied my email with it.
Then I used the script charmmlipid2amber.py in order to convert
the CHARMM-GUI formatted PDB file to the Amber Lipid14
formatted PDB file applying the command recommended
in the tutorial:
charmmlipid2amber.py -i step5_assembly.pdb -c
$AMBERHOME/AmberTools/src/etc/charmmlipid2amber/charmmlipid2amber.csv -o
out.pdb
The system returned with error message:
Error: Number of atoms in residue does not match number of atoms in
residue in replacement data file
I would appreciate any advice how to solve the problem.
Thank you,
Michael
*****************************
Michael Shokhen, PhD
Associate Professor
Department of Chemistry
Bar Ilan University,
Ramat Gan, 52900
Israel
email: michael.shokhen.gmail.com
email: shokhen.mail.biu.ac.il
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Received on Tue Apr 07 2015 - 23:30:03 PDT
