Hi,
Thanks for your suggestion about using ptraj via rst and then ambpdb, but it does not help.
There is probably an issue the way I mention the .mol2 for the non-standard residu in tleap. Is it enough to say "loadmol2 mol.mol2"? What don't I understand here?
So, to be complete,
tleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff99SB
mol = loadmol2 mol.mol2
loadamberparams test.frcmod
gaff = loadamberparams gaff.dat
complex = loadpdb test.pdb
and then we get:
Created a new atom named: H within residue: .R<0 1>
Created a new atom named: C within residue: .R<0 1>
Created a new atom named: C15 within residue: .R<0 1>
Created a new atom named: C16 within residue: .R<0 1>
Created a new atom named: C17 within residue: .R<0 1>
Created a new atom named: S within residue: .R<0 1>
Created a new atom named: C18 within residue: .R<0 1>
Created a new atom named: H11 within residue: .R<0 1>
Created a new atom named: H28 within residue: .R<0 1>
Created a new atom named: H29 within residue: .R<0 1>
Created a new atom named: O within residue: .R<0 1>
Created a new atom named: C19 within residue: .R<0 1>
Created a new atom named: C20 within residue: .R<0 1>
Created a new atom named: C21 within residue: .R<0 1>
Thanks,
Stefan
________________________________________
From: Daniel Roe [daniel.r.roe.gmail.com]
Sent: 23 January 2013 22:41
To: AMBER Mailing List
Subject: Re: [AMBER] Problem compatibility pdb in tleap
Hi,
I can think of two ways you might do this. You can try using cpptraj
to write the frame directly, which should write the proper TER cards
and atom/residue names. Alternatively, use ptraj/cpptraj to write out
the specified frame as an amber restart, then use ambpdb to convert
that restart to a PDB file.
-Dan
On Wed, Jan 23, 2013 at 2:32 PM, Stefan Knippenberg
<Stefan.Knippenberg.umons.ac.be> wrote:
> 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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>
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Thu Jan 24 2013 - 03:00:02 PST
