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

Una Bjarnadottir una.bjarnadottir at ucd.ie
Tue May 10 18:37:09 CEST 2005

Hi David,

Thank you for your advise, I have been checking it out how to modify the 
ffG43a1nb.itp file.  Could you be a little bit more specific how I would 
modify it. 
I'm not sure how to get the c6 and c12 values for the [atomtypes] and 
from my understanding I will get the c6 and c12 values for the 
[nonbond_params] and the [pairtypes] by using  these equation you gave 
c6[i][j] = sqrt (c6[i][i] * c6[j][j]) and
c12[i][j] = sqrt (c12[i][i] * c12 [j][j])
to get the c6 and c12 values in the .itp file.  But I don't have a clue 
on how to get the c6 and c12 values for the [atomtypes] anyway.  Is 
there a easy way to do it, could I find the values somewhere or could I 
use some of the files the PRODRG2 server generated and use them.  Also 
like it says in the manual p90 there is given a equation with the sigma 
and epsilon values, how would I get these values for my atom-types.  
Gromacs must have some files about these types because they are all on 
the list for different atom types which GROMACS uses!

Thank you in advance to anybody who could help me, Una

David wrote:

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
>gmx-users mailing list
>gmx-users at gromacs.org
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