On Tue, Oct 12, 2010, xuemeiwang1103 wrote:
> Thanks a lot for your help again. Atoms 9223 and 9224 are the
> hydrogen atoms of the same water molecule.Following your comments, I
> checked my PDB file carefully , then I found a problem . The first
> step is the building of residues. I created the new Lib files for my
> residues which coordinate to the metal ion.The I using the script
> <......saveamberparm xxx xxx.prmtop xxx.inpcrd
> but when I use the order: ambpdb -p xxx.prmtop<xxx.inpcrd>xxx.pdb &
> ,this PDB displays like :ATOM 9223 H1 H2O 578 47.112 46.701 54.456
> TER
> ATOM 9224 H2 H2O 578 47.436 48.165 54.674
> TER
> ATOM 9225 O H2O 578 47.744 47.282 54.881
> TER
We would have to know more about the exact commands you gave to leap in
setting up the prmtop file. You might play around with different orders of
doing things to see if you can get a pdb file (from ambpdb) without the TER
cards for residue 578.
...good luck...dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Oct 13 2010 - 07:30:06 PDT
