AMBER Archive (2004)

Subject: RE: AMBER: (no subject)

From: Ross Walker (
Date: Fri Jul 30 2004 - 16:09:25 CDT

Dear Hayden,

The problem is with the hydrogen's in your pdb file. Yours have the name

xHAx whereas xleap expects the format HAxx. Hence any hydrogen that starts
with a number instead of an H is being duplicated by xleap. Generally since
xleap will add missing hydrogens you are best off stripping all hydrogens
from your pdb file and then loading this into xleap. For all residues xleap
knows about it will then protonate them depending on their 'normal'
protonation state. This is why you need to rename histidine as either HID,
HIP HIE etc...

Anyway, I have attached several files for you that I have created with xleap
as follows (my nmr.1.pdb here has had the H's removed):

>xleap -s -f /usr/local/amber8/dat/leap/cmd/leaprc.ff99

Welcome to LEaP!
Sourcing: /usr/local/amber8/dat/leap/cmd/leaprc.ff99
Log file: ./leap.log
Loading parameters: /usr/local/amber8/dat/leap/parm/parm99.dat
Loading library: /usr/local/amber8/dat/leap/lib/all_nucleic94.lib
Loading library: /usr/local/amber8/dat/leap/lib/all_amino94.lib
Loading library: /usr/local/amber8/dat/leap/lib/all_aminoct94.lib
Loading library: /usr/local/amber8/dat/leap/lib/all_aminont94.lib
Loading library: /usr/local/amber8/dat/leap/lib/ions94.lib
Loading library: /usr/local/amber8/dat/leap/lib/solvents.lib
> nmr1 = loadpdb nmr.1.pdb
Loading PDB file: ./nmr.1.pdb
  total atoms in file: 264
  Leap added 265 missing atoms according to residue templates:
       265 H / lone pairs

   "So leap added 265 Hydrogens, you should check that this is indeed the
number you were expecting"

> bond nmr1.17.SG nmr1.34.SG
> bond nmr1.6.SG nmr1.33.SG
> bond nmr1.13.SG nmr1.27.SG

> savepdb nmr1 nmr.1.xleap_hydrogenated.pdb
Writing pdb file: nmr.1.xleap_hydrogenated.pdb
 Shortening residue name for PDB format: NASN -> ASN
 Shortening residue name for PDB format: CLYS -> LYS
> saveamberparm nmr1 nmr.1.prmtop nmr.1.inpcrd
Checking Unit.
WARNING: The unperturbed charge of the unit: 5.000000 is not zero.

 -- ignoring the warning.

Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameter
 total 104 improper torsions applied
Building H-Bond parameters.
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
  (Residues lacking connect0/connect1 -
   these don't have chain types marked:

        res total affected

        CLYS 1
        NASN 1
 (no restraints)
> saveoff nmr1 nmr.1.lib
 Creating nmr.1.lib
Building topology.
Building atom parameters.

So, I have saved you a pdb file that has the xleap added hydrogen atoms,
check these are correct. I have also saved you an OFF file (.lib) that can
be loaded back into leap with loadoff. This has the hydrogens added as well
as the 3 disulphide bonds created. The unit name in this OFF file is nmr1.

Your system has an overall charge of +5 so you should really charge
neutralise and solvate it before running MD. So use the lib file to do this
and create yourself new prmtop and inpcrd files that contain counter ions
and explicit water.

If you still have problems let me know what version of amber you are using
and if you have applied any of the bug fixes.

I hope this helps
All the best

|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- |
| | PGP Key available on request |

  • application/octet-stream attachment: nmr.1.pdb

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