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.
________________________________________________________________________
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
[email protected] [email protected] http://xray.bmc.uu.se/~spoel
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