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

David spoel at xray.bmc.uu.se
Mon May 9 20:08:13 CEST 2005

On Mon, 2005-05-09 at 17:54 +0100, Una Bjarnadottir wrote:
> 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? 

vanderwaals parameters and atom type definition.

> 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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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
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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