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

David van der Spoel spoel at xray.bmc.uu.se
Wed May 11 13:00:41 CEST 2005 

On Wed, 2005-05-11 at 11:47 +0100, Una Bjarnadottir wrote:
> Hi all,
> 
> David thanks for your respone!!
> I changed the files like you said but than grompp complained about next 
> new atom type in the ATP complex, CS1.  I added in 9 of the 47 atom 
> types to the .atp file in share/gromacs/top dir and I'm wandering if 
> they have all been replaced like OS to OA and where I could find 
> information about the new names if grompp will complain about the rest? 
In the gromos force field description (which is a book) or the papers,
or simply by comparing the ffgmx.atp and ffG43a1.atp files. It shouldn't
be necessary to add any new atomtypes at all.
> 
> These are the types I had to add in the .atp file;
>    OA (OS)  15.99940 ;     sugar or ester oxygen
>   CS1  13.01900 ;     sugar CH-group
>    HO  1.00800  ;     hydroxyl hydrogen
>  NR5*  14.00670 ;     aromatic N (5-ring, 3 bonds)
>  CR51  13.01900 ;     aromatic CH-group (5-ring), united
>   NR5  14.00670 ;     aromatic N (5-ring, 2 bonds)
>    CB  12.01100 ;     bare carbon (5-, 6-ring)
>   NR6  14.00670 ;     aromatic N (6-ring, 2 bonds)
> CR61  13.01900 ;     aromatic CH-group (6-ring), united
> 
> All my best to you, Una
> 
> On Tue, 2005-05-10 at 17:37 +0100, Una Bjarnadottir wrote:
> 
> >> 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 
> >> (http://www.gromacs.org/pipermail/gmx-users/2001-October/000124.html);
> >> 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!
> >  
> >
> 
> problem is that prodrg generates gromos87 force field while the new
> gromos 96 is slightly different. The OS (sugar oxygen) has been replaced
> by another oxygen (OA). If you modify your prodrg topology accordingly
> it should work. Check the *.atp files in  your share/top dir.
> 
> 
> >> 
> >> 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? 
> >>> >  
> >>> >
> >>    
> >>
> >> 
> >> ffG43a1nb.itp
> >> 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
> >>> >http://www.gromacs.org/mailman/listinfo/gmx-users
> >>> >Please don't post (un)subscribe requests to the list. Use the 
> >>> >www interface or send it to gmx-users-request at gromacs.org.
> >>> >
> >>    
> >>
> >> _______________________________________________
> >> gmx-users mailing list
> >> gmx-users at gromacs.org
> >> http://www.gromacs.org/mailman/listinfo/gmx-users
> >> Please don't post (un)subscribe requests to the list. Use the 
> >> www interface or send it to gmx-users-request at gromacs.org.
> >  
> >
> -- David. 
> ________________________________________________________________________ 
> 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 
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> 
> 
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
-- 
David.
________________________________________________________________________
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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

More information about the gromacs.org_gmx-users mailing list