Yes, you will be able to solvate that structure. You should still relax and
heat the system slowly, then equilibrate it so that the waters settle down.
On Thu, Jan 13, 2011 at 9:19 AM, Baptiste Legrand <bap.legrand.gmail.com>wrote:
> I load the prepin from my sirius file and the pdb resulting from my MD
> in vacuum and then I will have the structure from my MD in vacuum but
> solvated and ready for a new MD simulations?
>
> Le 13/01/2011 15:09, Jason Swails a écrit :
> > 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
> >>>>>
> >>>>> _______________________________________________
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> >>>> _______________________________________________
> >>>> AMBER mailing list
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> >>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>
> >>>
> >>
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> >>
> >
> >
>
>
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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 - 07:00:07 PST
