I thank you very much David for your recommendations.
George
> 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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>
--
*---------------------------------------------*
|Dr George Lamprinidis |
|Researcher & Laboratory Assistant Staff |
|School of Health Sciences |
|Faculty of Pharmacy |
|National & Kapodistrian University of Athens |
|Greece |
|tel: +30 2107274304 |
| +30 2107274521 |
|fax: +30 2107274747 |
|e-mail: lamprinidis.pharm.uoa.gr |
| geolampr.gmail.com |
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Received on Fri Aug 02 2013 - 00:30:03 PDT
