That shouldn't be necessary -- just load the prepin file you have from last
time
On Thu, Jan 13, 2011 at 8:53 AM, Baptiste Legrand <bap.legrand.gmail.com>wrote:
> I have created a pdb/mol2 template file using sirius and then I have
> run antechamber before starting a MD in vacuum. So I have just the
> initial prepin file and the corresponding prmtop and inpcrd.
> Perhaps, a solution may be to create a pdb from my final rst file and
> then to launch a second time antechamber to have the prepin from this
> file (with the good coordinates) before the MD in explicit solvent?
>
> Baptiste
>
> Le 13/01/2011 14:31, Jason Swails a écrit :
> > 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
> >>>
> >>> _______________________________________________
> >>> AMBER mailing list
> >>> AMBER.ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jan 13 2011 - 06:30:03 PST
