Hi everybody,
>From your answers, I understood I should have loaded a mol2 file - thanks for the suggestion (loadmol2 mol.mol2).
But still, it does not work and the problem in tleap ("Created a new atom named: C165 within residue: .R<0 1>") is the same...
The pdb I spoke about below was created using ptraj. I do not understand how I can use ambpdb to take frame 942 from the .mdcrd file.
Any further ideas? With (small) molecules, I would try antechamber, but I cannot use it here (DNA+nonstandard molecule)...
Thanks for any help!
Bye,
Stefan
________________________________________
From: David A Case [case.biomaps.rutgers.edu]
Sent: 23 January 2013 19:55
To: AMBER Mailing List
Subject: Re: [AMBER] Problem compatibility pdb in tleap
On Wed, Jan 23, 2013, Stefan Knippenberg wrote:
>
> Willing to solvate a system which has been running in production run for
> something like 100 ns, I got stuck by reading the pdb file in tleap:
>
> Created a new atom named: C165 within residue: .R<0 1>
You don't say how you made the pdb file.
> The pdb I started from is the final structure of a previous calculation,
> and reads like
>
> ATOM 233 7C16 0 1 171.290 58.160 51.330 0.00 0.00
But no standard amino acids or nucleic acids have atoms names like the above,
and you have a residue named "0" (zero), rather than a real residue name. So,
you will have to correctly generate a pdb file (use ambpdb), and you will have
to load the topology library (.lib, .mol2 or similar file) for the
non-standard residue. It is not enough just to load the frcmod file.
...dac
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Received on Wed Jan 23 2013 - 14:00:02 PST
