[gmx-users] adding h2po4 to system

David van der Spoel spoel at xray.bmc.uu.se
Thu May 13 22:18:18 CEST 2010

On 5/13/10 8:31 PM, Tiago Barros wrote:
> 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 
> field?
Since I made the itp file, it probably needs to be updated to new top 
format. If you check the file it has

[ bonds ]
;  ai    aj funct           c0           c1
     5     1     1 1.637000e-01

so a force constant has to be added.

> Is there a more appropriate way to include PO4 residues from crystal 
> structures?
> Many thanks,
> Tiago

David van der Spoel, PhD, Professor of Biology
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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