Did you not have an amber prep or OFF library file for residue UNK when you
first created the topology file? It's these library files that provides the
atom name -> atom type mapping needed here.
Good luck,
Jason
On Thu, Jan 13, 2011 at 4:15 AM, Baptiste Legrand <bap.legrand.gmail.com>wrote:
> Thanks Jason and Bill for your reply.
> This is my 'leap.in' file:
> source leaprc.gaff
> source leaprc.ff99SB
> UNK=loadpdb sa2_ct_12.pdb
> loadamberparams sa2_ct_12.frcmod
> solvatebox UNK TIP3PBOX 8 0.75
> saveamberparm UNK ./wat/prep/sa2_ct_12.prmtop ./wat/prep/sa2_ct_12.inpcrd
>
> And thes errors in the leap.out:
> ...
> FATAL: Atom .R<UNK 1>.A<H10 85> does not have a type.
> FATAL: Atom .R<UNK 1>.A<H26 86> does not have a type.
> FATAL: Atom .R<UNK 1>.A<C30 87> does not have a type.
> FATAL: Atom .R<UNK 1>.A<H7 88> does not have a type.
> FATAL: Atom .R<UNK 1>.A<H19 89> does not have a type.
> Failed to generate parameters
> Parameter file was not saved.
>
> The errors may come from the fact that that my peptide is modified and
> was generated first by antechamber (for the calculations in vacuum). So,
> as the nomenclature is not standard, leap cannot find the atom type for
> each atom in its library?
>
>
>
>
>
> Le 12/01/2011 20:22, Bill Ross a écrit :
> >> I want to use structures from a previous MD run in vacuum to launch a
> >> run in a solvent box. Is it possible to load directly my rst and prmtop
> >> files in leap to create "solvated" starting files?
> >> For the moment, I have convert the rst files in pdb using ambpdb
> >> nevertheless the generated pdb don't have the 'atom type' column and
> >> cannot be loaded in leap.
> > You need to use the pdb, loadpdb, solvate, and saveamberparm.
> > There is no such thing as an 'atom type' column in pdb that
> > leap requires. If you have the same setup as when you generated
> > the vacuum saveamberparm, the pdb should load ok. If you send
> > whatever error/warning messages you are seeing, we can diagnose
> > directly.
> >
> > Bill
> >
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Thu Jan 13 2011 - 06:00:02 PST
