Hello Amber Community,
I tried to load pdb file into xleap. i find there are difficulties of
importing a file
from pdb bank or a pdb file, which is recognized from InsightII or
Discovery, into xleap.
Can anyone help with pdb file format, which is acceptable to amber and
help see the problem below:
I attached my pdb file. After i run xleap:
$amber10/exe/xleap -f $amber10/dat/leap/cmd/leaprc.ff99SB
i loaded pdb file into xleap:
-----------------------------------------
>lyz=loadpdb model.pdb
Loading PDB file: ./model.pdb
Created a new atom named: HB1 within residue: .R<NLYS 1>
Created a new atom named: HG1 within residue: .R<NLYS 1>
Created a new atom named: HD1 within residue: .R<NLYS 1>
Created a new atom named: HE1 within residue: .R<NLYS 1>
Created a new atom named: HB1 within residue: .R<PHE 3>
Created a new atom named: HA1 within residue: .R<GLY 4>
....
total atoms in file: 1961
Leap added 163 missing atoms according to residue templates:
163 H / lone pairs
The file contained 156 not in residue templates
-----------------------------------------------
I am very confused what these "163 H / lone pairs" mean.
Can I stop these addings if I want to keep my desired protonation state?
What is wrong about my pdb file format?
Thanks
Jim
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Received on Fri Feb 05 2010 - 01:30:02 PST
