i am using tleap not xleap
On Tue, Feb 15, 2011 at 6:20 PM, peker milas <pekermilas.gmail.com> wrote:
> Hi Vani,
>
> Did you check atom types in your molecule using xleap according to parm99
> file ?
>
> peker
>
> On Tue, Feb 15, 2011 at 7:02 PM, vani panguluri <vanipanguluri.gmail.com>
> wrote:
> > Hello,
> >
> > while loading the pdbfile it was displaying the following messages
> > Created a new atom named: HN within residue: .R<LEU 544>
> > Created a new atom named: 1HB within residue: .R<ALA 545>
> > Created a new atom named: 2HB within residue: .R<ALA 545>
> > Created a new atom named: 3HB within residue: .R<ALA 545>
> > Created a new atom named: HN within residue: .R<ALA 545>
> > Created a new atom named: 1HB within residue: .R<SER 546>
> > Created a new atom named: 2HB within residue: .R<SER 546>
> > Created a new atom named: HN within residue: .R<SER 546>
> > Created a new atom named: 1HB within residue: .R<ALA 547>
> > Created a new atom named: 2HB within residue: .R<ALA 547>
> > Created a new atom named: 3HB within residue: .R<ALA 547>
> > Created a new atom named: HN within residue: .R<ALA 547>
> > Created a new atom named: HN within residue: .R<CVAL 548>
> > total atoms in file: 1486
> > Leap added 413 missing atoms according to residue templates:
> > 413 H / lone pairs
> > The file contained 409 atoms not in residue templates
> > *While running this step i got this error*
> > saveamberparm apocynin 1k4uapo_1.prmtop 1k4uapo_1.inpcrd
> > Checking Unit.
> > WARNING: The unperturbed charge of the unit: -2.999900 is not zero.
> > FATAL: Atom .R<ALA 547>.A<1HB 11> does not have a type.
> > FATAL: Atom .R<ALA 547>.A<2HB 12> does not have a type.
> > FATAL: Atom .R<ALA 547>.A<3HB 13> does not have a type.
> > FATAL: Atom .R<ALA 547>.A<HN 14> does not have a type.
> > FATAL: Atom .R<CVAL 548>.A<HN 18> does not have a type.
> > Failed to generate parameters
> > Parameter file was not saved.
> >
> > I had used leaprc.ff99SB also i am getting can any one suggest me a
> > solution...........
> >
> > i want to Create topology and coordinate files for 1k4uapo complex i am
> > getting the above error .......
> >
> >
> > Regards,
> > Vani
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> >
>
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Received on Tue Feb 15 2011 - 17:00:02 PST
