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

Una Bjarnadottir una.bjarnadottir at ucd.ie
Wed May 11 12:47:39 CEST 2005 

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? 

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 The OS (sugar oxygen) has been replaced
by another oxygen (OA).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.
>>> >
>>    
>>
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>  
>
-- 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 
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