[gmx-users] Atom Types, grompp problem!!
una.bjarnadottir at ucd.ie
Mon May 9 18:54:24 CEST 2005
I have been following both the GROMACS manual (chapter 5), and the
mailing list on how to add in the rest of the atom types which GROMACS
uses (47 different atom types in the manual).
I am using the *ffG43a1p *force field and was adding in ATP to my
enzyme. I added in the atom types which were missing (CR61, OS, CS1,
HO, NR5*, CR51, NR5, CR, NR6) to the .atp file for the force field but
didn't change the .rtp file because it says in the manual that it's
better not to change that, but change instead the .top file which I did.
There I added in the #include ".itp" statement and added in the ATP in
to "[ molecules ]" statement last in the .top file.
I generated the DRGFIN.GRO and the DRGGMX.ITP for the ATP using the
Dundee PRODRG2 Server and updated the .gro file with the DRGFIN.GRO
file, by pasting the coordinates onto the end of the .gro file generated
by pdb2gmx program and changed the numbers at the top and put it to the
right order at the bottom and saved it.
Everything goes allright until I use the grompp command, than it says
"Atomtype 'OS' not found!" and OS is the first of the atomtypes in the
ATP which I had to add to the .atp file.
So what can be wrong, will I have to modify some other files than the
.atp in the forcefield like the hydrogen database or the termini database?
And also I'm following the Gromacs Drug/Enzyme complex solvation
tutorial and there the drug has the atom type OS in the .itp file from
dundee PRODRG2 server and uses the normal force constant and there are
The problems in the mailing list are usually when people are adding in
atom types which are not already recognizable by GROMACS so I must be
doing something really silly or really little wrong but I just can't
figure it out. So can please somebody help me and tell if I am
forgetting to change something and I will really appreciate it:)
Best regards, Una
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