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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Received on Tue Feb 15 2011 - 16:30:03 PST
