On Thu, Aug 01, 2013, Giorgos Lamprinidis wrote:
> 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.
Recommended, esp. if this is not a one-off event:
Ask on the CHARMM blog site how they convert CHARMM protein pdb files
to PDB (version3) standard. I think most people use the mmtsb toolkit, but
there may be other scripts as well. Use what they recommend.
OR, remove all the hydrogen atoms from the protein part of your pdb file;
that will leave you with a relatively small number of problem atoms -- ILE
CD, probably some others. Note that CHARMM uses HSD, HSE for what Amber calls
HID, HIE. (The PDB wants to call these HIS_LL_DHD1, HIS_LL_DHE2, but neither
Amber nor CHARMM can really deal with 11-character residue names.) I'd
suggest splitting of the protein part, loading that into tleap, and keep
modifying the atom names until LEaP stops complaining.
[Note: I was unable to read the leap.log file you attached...but the pdb file
looks fine except for the old-fashioned atom names.]
...dac
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Received on Thu Aug 01 2013 - 14:00:02 PDT
