[gmx-users] protein in SDS/water

Anna Marabotti anna.marabotti at isa.cnr.it
Wed Jun 17 09:11:13 CEST 2009

Dear gmx-users,
I would like to setup a simulation of a protein in a mixture SDS/water using GROMACS 3.3.1. 
I proceeded in this way:

- after pdb2gmx, I created with editconf a cubic box of 10 nm per side centered on my protein:
editconf -f my_prot.gro -o my_prot_box.gro -bt cubic -box 10 -c

- then I used genbox to fill the box with water and to add the desired quantity of SDS (to simulate 3.5 M SDS
I added approx. 2000 molecules of SDS to the box). I obtained the coordinates of SDS from a pdb file and then
used PRODRG server to create the topology and the coordinate in .gro format. The command was:
genbox -cp my_prot_box.gro -cs spc216.gro -ci SDS.gro -nmol 2000 -o my_prot_boxsolv.gro -p my_prot.top

The output of this command is a .gro file in which the protein is at the centre of the cubic box, filled with
approx. 36000 water molecules and 2000 molecules of SDS. I had a look at it with VMD, and all seems to be OK.
The only "strange" thing is that the SDS molecules are not considered as "solvent" molecules.

The problem comes when I'm starting to minimize this box. When I use grompp:
grompp -f em.mdp -c my_prot_boxsolv.gro -o my_prot_mini.tpr -p my_prot.top

the program returns the error:
Fatal error:
number of coordinates in coordinate file (my_prot_boxsolv.gro, 144801) does not match topology (my_prot.top,

I tried to manually edit the .top file by adding the number of SDS molecules under the section [ molecules ],
I also added manually "SDS.itp" to the topology file, but all was useless. I don't really know especially why
GROMACS claims that the number of coordinates in the topology is 0, since at least the protein is present. 
What's wrong? I saw many procedures to create mixed solvents for a simulation, but I don't know what is the
better one. However, genbox -nmol -ci seems perfect for me and apparently it functions in creating the system.
So why the topology file is not updated by genbox? Or in case, could you suggest me a better procedure to add
3.5 M SDS to my protein in water?

Thank you and best regards

I tried to copy the .top file at the end of the message, but it is too big, so please if you need to see it
let me know how to send to you.

Anna Marabotti, Ph.D.
Laboratory of Bioinformatics and Computational Biology
Institute of Food Science, CNR
Via Roma 64
83100 Avellino (Italy)
Phone: +39 0825 299651
Fax: +39 0825 781585
Skype: annam1972
E-mail: amarabotti at isa.cnr.it
Web page: http://bioinformatica.isa.cnr.it/anna/anna.htm
"If you think you are too small to make a difference, try sleeping with a mosquito"

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