[gmx-users] Atom Types, grompp problem!!

Una Bjarnadottir una.bjarnadottir at ucd.ie
Mon May 9 18:54:24 CEST 2005

Hi hi,

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 
no complains!

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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