Dac please find attached the leap.log file together with the output pdb file
"step5_assembly_rhodopsin_refined_1.pdb " from charmmlipid2amber.x scripts.
I have deleted a lot of lipids from pdb file to reduce the size of it.
George
-----Original Message-----
From: David A Case [mailto:case.biomaps.rutgers.edu]
Sent: Πέμπτη, 1 Αυγούστου 2013 4:45 μμ
To: AMBER Mailing List
Subject: Re: [AMBER] Charmmgui pdb file error
On Thu, Aug 01, 2013, Giorgos Lamprinidis wrote:
>
> So I downloaded the step5_assembly.pdb file, I converted it using
> charmmlipid2amber.x script and as the examples says, I tried to load
> the pdb file to tleap using leaprc.lipid11 and leaprc.ff99SB force field
files.
>
> However I get errors for the protein part.
Many such errors are really easy to fix (e.g. CHARMM uses out-dated atom and
residue names). But without knowing what sorts of errors you are getting,
the list cannot be of much help.
...dac
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Received on Thu Aug 01 2013 - 08:00:02 PDT
