[AMBER] bad atom type: IP MMPBSA.py sodium Na+ ion [SOLVED]

From: Oliver Grant <olivercgrant.gmail.com>
Date: Fri, 14 Jan 2011 11:03:30 +0000

Hi AMBER users,

Just for the record. The patch fixed my problem.
Thanks Jason :)

Hi Jason,

I'm simulating a carbohydrate bound to a protein with a Na+ ion bridging
between the protein and the carbohydrate. I've successfully run MMPBSA.py
excluding the Na+ atom with both PB and GB and decomp:

But now when I include the Na+ ion I get this in my out file:

$ more mmpbsa.py.log
ptraj found! Using /array2/programs/amber11_20100607/bin/ptraj
sander found! Using /array2/programs/amber11_20100607/bin/sander

Preparing trajectories with ptraj...
11 frames were read in and processed by ptraj for use in calculation.

Starting calculations...

Starting gb calculation...

  calculating ligand contribution...
  calculating receptor contribution...
 bad atom type: IP
  calculating complex contribution...
 bad atom type: IP
Starting pb calculation...

  calculating ligand contribution...
  calculating receptor contribution...
  calculating complex contribution...

Calculations complete. Writing output file(s)...

Error: No potential terms in sander output! Check output files.
NOTE: All files have been retained for debugging purposes. Type MMPBSA.py
--clean to erase these files.

I've checked the amber mailing list but the only recommendations I could
find were to remove the Na+ ion, but I need to include it.

Any help would be great,


This is due to the fact that the radius of the sodium atom is not defined in
the sander source code (see lines around 1845 of
$AMBERHOME/src/sander/mdread.f). I've attached a patch that adds in a
radius of 1.16 (angstroms) for the sodium ion plus a 1.4 angstrom probe
radius which should fix your issue. However, this will only affect sodium
atoms whose type is IP (which is not true for newer ion models, such as
ions08.lib, etc.).

Apply this patch from $AMBERHOME like

patch -p0 -N < sodium_gb.patch

and recompile sander in serial.

Hope this helps,

Here is the contents of the patch, I'm not sure if attachments get archived:
more sodium_gb.patch
--- src/sander/mdread.f 2010-04-26 08:21:23.000000000 -0400
+++ src/sander/mdread.f 2011-01-12 16:22:07.801623229 -0500
.@ -1841,6 +1841,8 @@
                ! Mg radius = 1.18A: ref. 30 in J. Chem. Phys.
 107, 5422
                ! Mg radius = 1.45A: Aqvist 1992
                x(L165-1+i) = 1.18d0 + 1.4d0
+ else if (atype(1:2) == 'IP') then
+ x(L165-1+i) = 1.16d0 + 1.4d0
                write( 0,* ) 'bad atom type: ',atype
                call mexit( 6,1 )

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Received on Fri Jan 14 2011 - 03:30:02 PST
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