[gmx-users] box of water with ions

[David van der Spoel]

Victor Manuel Rosas-Garcia wrote:
> Hello everybody,
> 
> I'm trying to build a water box with some calcium carbonate in it but, for the
> life of me, I cannot get it right.  I can build a box of water with CaCl
> without any problems.  I have a grompp.mdp file and then:
> 
> genbox -box 2 2 2 -cs spc216 -o h2o.gro
> pdb2gmx -f h2o.gro -q h2o.pdb -n index.ndx
> grompp -f grompp.mdp -c h2o.gro -n index.ndx -p topol.top -o topol.tpr
> mdrun -v
> genion -s topol.tpr -o out.gro -pname Ca -pq 2 -np 5 -nname Cl -nq -1 -nn 10
> 
> and then pdb2gmx... mdrun...  No problem there.

you shoulnd't use pdb2gmx for other stuff than proteins. check chapter 5 
in the manual
> 
> I am aware that genion cannot introduce polyatomic ions so, to generate a box
> of water with CaCO3 I tried to introduce the anion first with genbox and then
> the Ca with genion (I have CO2(-2) as a pdb file):
> 
> genbox -box 2 2 2 -cs spc216 -ci co3.pdb -nmol 10
> pdb2gmx -f out.gro -q out.pdb -n index.ndx
> 
> and I got the following error message:
> [snip, snip]
> -------------------------------------------------------
> Program pdb2gmx, VERSION 3.3
> Source code file: resall.c, line: 438
> 
> Fatal error:
> Residue 'DRG' not found in residue topology database
> 
> -------------------------------------------------------
> 
> So, I tried x2top:
> x2top -f out.gro -o topol.top
> 
> and then I got
> [snip, snip]
> -------------------------------------------------------
> Program x2top, VERSION 3.3
> Source code file: futil.c, line: 537
> 
> Fatal error:
> Library file ffG43a1.n2t not found in current dir nor in default directories.
> (You can set the directories to search with the GMXLIB path variable)
> -------------------------------------------------------
> 
> so, neither pdb2gmx nor x2top worked.  I submitted CO3(-2) to the prodrg server
> and I have all the files, but it gave me SIX *.TOP files so, I don't really
> know which one to use.  None of them seem (to me) to fit the format of the
> gromacs topology files I saw in the gromacs documentation.  Needless to say, I
> am FAR from being an experienced gromacs user, although I do have experience in
> computational chemistry, just not molecular dynamics.
> 
> Any recommendations?  
> 
> 
> 
> Victor M. Rosas García, PhD
> Coordinador del Posgrado en Ciencias
> Facultad de Ciencias Quimicas, UANL
> e-mail: quimico69 at yahoo.com
> Tel: (81) 8329-4010 ext. 6253
> Fax: (81) 8376-5375
> 
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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://folding.bmc.uu.se
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