is ist possible to use antechamber to get the parameters for this non standard residue or I have to use RED?
Urszula
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Von: David A Case [case.biomaps.rutgers.edu]
Gesendet: Donnerstag, 3. November 2011 19:06
An: AMBER Mailing List
Betreff: Re: [AMBER] problems in reading molecule in tleap/xleap
On Thu, Nov 03, 2011, Urszula Uciechowska wrote:
>
> I have a mol2 its a peptide (see attachment), I can also have it as a pdb file
> but I got the same errors,
> after loading to the xleap/tleap I am getting errors:
Your mol2 file is quite odd. The residue that claims to be PHE has
a weird 5-membered ring on the side chain. I'd suggest converting to pdb
format, looking carefully at the structure in a visual editor to make sure
it is really what you want. If you have a non-standard amino acid, you will
have to give it a name that doesn't conflict with the standard ones (can't be
PHE) and you will have to generate a library file for it.
If you are new to amber, try running a standard peptide first, to be sure you
understand how things work, before tackling this structure.
...good luck...dac
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Received on Fri Nov 04 2011 - 02:00:02 PDT
