AMBER Archive (2004)

Subject: AMBER: How to add H+ ion in leap?

From: xinchen (xinchen_at_ic.sunysb.edu)
Date: Tue Feb 17 2004 - 13:46:10 CST

Hello,

I tried to add H+ to a pdb file using the code below, it seems fine, but
when I tried to save to pdb file, it failed as "Segmentation fault". Any
suggestions? Anyone have experience on add H+ ion to a solution? I am
using AMBER 7 and Mandrake Linux 9.2. Thanks a lot.

$ tleap
-I: Adding /usr/local/amber7/dat/leap/prep to search path.
-I: Adding /usr/local/amber7/dat/leap/lib to search path.
-I: Adding /usr/local/amber7/dat/leap/parm to search path.
-I: Adding /usr/local/amber7/dat/leap/cmd to search path.

Welcome to LEaP!
(no leaprc in search path)
> source leaprc.ff94
----- Source: ./leaprc.ff94
----- Source of ./leaprc.ff94 done
Log file: ./leap.log
Loading parameters: /usr/local/amber7/dat/leap/parm/parm94.dat
Loading library: /usr/local/amber7/dat/leap/lib/all_nucleic94.lib
Loading library: /usr/local/amber7/dat/leap/lib/all_amino94.lib
Loading library: /usr/local/amber7/dat/leap/lib/all_aminoct94.lib
Loading library: /usr/local/amber7/dat/leap/lib/all_aminont94.lib
Loading library: /usr/local/amber7/dat/leap/lib/ions94.lib
Loading library: /usr/local/amber7/dat/leap/lib/solvents.lib
> x1 = loadpdb 1UBQ.pdb
Loading PDB file: 1UBQ.pdb
  total atoms in file: 660
  Leap added 745 missing atoms according to residue templates:
       745 H / lone pairs
> hp = createatom HP HW 1.000
> set hp element H
> hpp = createunit hpp
> add hpp hp
> addions x1 hpp 1
Adding 1 counter ions to "x1" using 1A grid
Grid extends from solute vdw + 0.00 to 6.00
Resolution: 1.00 Angstrom.
grid build: 0 sec
Solvent present: replacing closest with ion
         when steric overlaps occur
Calculating grid charges
charges: 3 sec
(No solvent overlap)
Placed hpp in x1 at (32.44, 27.89, -1.37).

Done adding ions.
> savepdb x1 xx.pdb
Writing pdb file: xx.pdb
Segmentation fault

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu