[gmx-users] protein in SDS/water

Mark Abraham Mark.Abraham at anu.edu.au
Wed Jun 17 09:29:30 CEST 2009

Anna Marabotti wrote:
> 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.

Shrug... that depends on the definition of solvent.

> 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,
> 0)

OK, so probably something is wrong with your [molecules] section.

> 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. 

Not if [molecules] is mangled. The order of the directives is quite 
important. The #include for SDS.itp must come before [molecules] and 
after the final subsection of any other [molecule] section. See parts of 
chapter 5 of the manual.


> 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
> Anna
> 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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