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
> _______________________________________________
> 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
Received on Tue Feb 15 2011 - 16:30:04 PST
