[gmx-users] box of water with ions

Victor Manuel Rosas-Garcia quimico69 at yahoo.com
Sat Sep 2 02:16:41 CEST 2006

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.

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

Do You Yahoo!?
Tired of spam?  Yahoo! Mail has the best spam protection around 

More information about the gromacs.org_gmx-users mailing list