[gmx-users] problem with adding a carbonate molecule to .rtp file

[David van der Spoel]

On Sun, 2005-03-06 at 08:59 +0000, balamurugan r wrote:
>   Sir,

> and then i tried to update the ff<***>.rtp file by adding the
> following lines to the last of the .rtp file 
> [CO3]
> [atoms]
> OAA OM  -0.221  0
> CAC  C  0.494  1
> OAB  OM  -0.221 0
> OAD  OM  -0.052 2
>   I obtained the details from the .itp file from PRODRG2 server
> but still i am not able to run pdb2gmx the error is that :
>   "Atom C in residue CO3 330 not found in rtp entry with 4 atoms while
> sorting atoms "
> 
>   I dont know how to proceed further. 
> please guide me where i went wrong
You're almost there. The first string in the rtp entry is the atom name
as it appears in the pdb file, the second is the atom type. You probably
need to change the first string to match the pdb file.

Besides that you need to carefully check the force field for the CO3
group. I would suggest you do a simulation of it in pure water as well
to test whether geometry is reasonable, and e.g. hydrogen bonding
distances.
> 
> 
> 
> 
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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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-- 
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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