The charmmlipid2amber.x file was only ever designed to convert Lipid
residues from Charmm naming over to AMBER naming - it ignores amino acids.
In principle we could add functionality to convert the amino acids over to
iupac naming but ideally what would be better is to try to make a more
comprehensive 'pdb' cleaner for AMBER that is smart and can convert
multiple inputs into what AMBER expects. Perhaps a nice summer project for
a good student.
All the best
Ross
On 5/7/13 3:44 PM, "David A Case" <case.biomaps.rutgers.edu> wrote:
>On Tue, May 07, 2013, Dipankar Roy wrote:
>>
>> ated a new atom named: HG1 within residue: .R<SER 420>
>> Joining SER - ILE
>> Created a new atom named: HN within residue: .R<ILE 421>
>> Created a new atom named: HG11 within residue: .R<ILE 421>
>> Created a new atom named: CD within residue: .R<ILE 421>
>> Created a new atom named: HD1 within residue: .R<ILE 421>
>> Created a new atom named: HD2 within residue: .R<ILE 421>
>> Created a new atom named: HD3 within residue: .R<ILE 421>
>
>You have CHARMM=like atom names, but Amber uses IUPAC (and PDB version 3)
>names. Google on "convert charmm atom names to amber" for some tools
>that can
>help with the conversion.
>
>(I don't know why charmmlipid2amber.x is not doing this.)
>
>...dac
>
>
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Received on Tue May 07 2013 - 17:00:02 PDT
