[AMBER] To convert the CHARMM-GUI formatted .pdb file into Lipid14 formatted .pdb file

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From: Shreeramesh <shreeramesh.gmail.com>
Date: Fri, 15 Apr 2016 04:27:48 -0700

Dear Sir,

I have to run MD for lipid bilayer composed of DOPC. I built a model
structure in CHARMM-GUI and I want to convert the CHARMM-GUI formatted .pdb
file into Lipid14 formatted .pdb file for the purpose of running tleap

I use the following script for the conversion and was unsuccessful. I
attached (i) the CHARMM-GUI generated structure (rec.pdb) and (ii) tleap
script (tleap.all) in attachment

Please kindly help me to convert the CHARMM-GUI generated structure
into Lipid14
formatted .pdb file

Script employed for the conversion as given in AMBER tutorial:

http://ambermd.org/tutorials/advanced/tutorial16/

*charmmlipid2amber.py –i rec.pdb [-c substitution_definitions.csv] \ -o
rec2.pdb*

Thanks & regards

*Ramesh M*
Email: shreeramesh.gmail.com
Mobile: (91) + 9646469938 (27) + (0) 844556164

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chemical/x-pdb attachment: rec.pdb

application/octet-stream attachment: tleap.all

Received on Fri Apr 15 2016 - 04:30:03 PDT