[gmx-users] adding h2po4 to system

Tiago Barros tiago at me.com
Thu May 13 20:31:35 CEST 2010

Dear all,

There was a similar thread in the archives, but I could not find the  
solution to my problem from the only reply (nor in the manual).

I've been trying to add 3 h2po4 ions to my system, as these appear to  
be tightly bound to the protein I want to use in my calculations.

I got hold of a h2po4.gro file (from the mailing list archive) and  
used genbox to successfully had 3 h2po4 molecules to the system. My  
idea was to then change the coordinates my hand in other to match the  
position of the 3 PO4 residues from the crystal structure. As I want  
to use the ffG43a1 force field, I made a modified copy (PO4.itp) of  
the h2po4.itp file so that the atomtype "HO" was modified to "H" (as  
in ffG43a1.atp; but this I already found suspicious). I then added  
#include "PO4.itp" right after the #include "ions.itp" and added "PO4   
3" to the end of the .top file.

grompp stops with the error:

Program grompp, VERSION 4.0.7
Source code file: toppush.c, line: 1379

Fatal error:
Incorrect number of parameters - found 1, expected 2 or 4 for Bond.

Is the 'h2po4.itp" file not appropriate to use with the ffG43a1 force  

Is there a more appropriate way to include PO4 residues from crystal  

Many thanks,


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