[gmx-users] Re: protein in SDS/water
Anna Marabotti
anna.marabotti at isa.cnr.it
Wed Jun 17 15:05:55 CEST 2009
Dear Mark,
thank you very much for suggestions. I'm pasting here an "extract" of the .top file I used during the grompp
process (the complete one is too big to be sent to the mailing list, as I told yesterday - the dots indicate
that I delete the information here, but they are present in the original file). As you can see, I added
manually the #include for SDS.itp before [ molecules ] and "SDS" under [ moleculetype ] and [ molecules ]
section. Maybe I made a trivial error, but I can't find it. All lines under [ atoms], [bonds], [pairs],
[angles] and [dihedral] sections refer only to the protein.
Moreover, it is quite strange to me that when I'm doing genbox, the top file is not updated automatically. I
copied the SDS.itp file from PRODRG in the directory ../gromacs/share/top containing all others .itp files,
but it seems that the program does not find information for SDS to include automatically in the .top file
Many thanks for help
Kind regards
Anna
Here the my_prot.top file (extract):
;
; File 'my_prot.top' was generated
; By user: anna (62867)
; On host: bioserv1.isa.cnr.it
; At date: Tue Jun 16 16:15:08 2009
;
; This is your topology file
; "The World is a Friendly Place" (Magnapop)
;
; Include forcefield parameters
#include "ffG43a1.itp"
[ moleculetype ]
; Name nrexcl
Protein 3
SDS 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB chargeB massB
1 NL 1 SER N 1 0.129 14.0067 ; qtot 0.129
2 H 1 SER H1 1 0.248 1.008 ; qtot 0.377
3 H 1 SER H2 1 0.248 1.008 ; qtot 0.625
.........................................................................................
.........................................................................................
2280 C 229 GLU C 980 0.27 12.011 ; qtot -6.73
2281 OM 229 GLU O1 980 -0.635 15.9994 ; qtot -7.365
2282 OM 229 GLU O2 980 -0.635 15.9994 ; qtot -8
[ bonds ]
; ai aj funct c0 c1 c2 c3
1 2 2 gb_2
1 3 2 gb_2
1 4 2 gb_2
1 5 2 gb_20
.......................................................
.......................................................
2275 2276 2 gb_26
2276 2277 2 gb_26
2277 2278 2 gb_5
2277 2279 2 gb_5
2280 2281 2 gb_5
2280 2282 2 gb_5
[ pairs ]
; ai aj funct c0 c1 c2 c3
1 7 1
1 10 1
1 11 1
...................................
...................................
2273 2275 1
2273 2280 1
2274 2277 1
2275 2278 1
2275 2279 1
2275 2281 1
2275 2282 1
2276 2280 1
[ angles ]
; ai aj ak funct c0 c1 c2 c3
2 1 3 2 ga_9
2 1 4 2 ga_9
2 1 5 2 ga_10
3 1 4 2 ga_9
3 1 5 2 ga_10
.....................................
.....................................
2275 2276 2277 2 ga_14
2276 2277 2278 2 ga_21
2276 2277 2279 2 ga_21
2278 2277 2279 2 ga_37
2274 2280 2281 2 ga_21
2274 2280 2282 2 ga_21
2281 2280 2282 2 ga_37
[ dihedrals ]
; ai aj ak al funct c0 c1 c2 c3 c4
c5
2 1 5 9 1 gd_14
1 5 6 7 1 gd_17
1 5 9 11 1 gd_20
5 6 7 8 1 gd_12
5 9 11 13 1 gd_4
..............................................
..............................................
2270 2272 2274 2280 1 gd_19
2272 2274 2275 2276 1 gd_17
2272 2274 2280 2282 1 gd_20
2274 2275 2276 2277 1 gd_17
2275 2276 2277 2279 1 gd_20
[ dihedrals ]
; ai aj ak al funct c0 c1 c2 c3
5 1 9 6 2 gi_2
9 5 11 10 2 gi_1
11 9 13 12 2 gi_1
14 13 16 15 2 gi_1
16 14 18 17 2 gi_1
18 16 20 19 2 gi_2
20 18 22 21 2 gi_1
..........................................
..........................................
2260 2256 2258 2261 2 gi_1
2262 2249 2264 2263 2 gi_1
2264 2262 2266 2265 2 gi_1
2266 2264 2270 2267 2 gi_2
2270 2266 2272 2271 2 gi_1
2272 2270 2274 2273 2 gi_1
2274 2272 2280 2275 2 gi_2
2276 2279 2278 2277 2 gi_1
2280 2274 2282 2281 2 gi_1
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif
; Include water topology
#include "spc.itp"
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif
; Include generic topology for ions
#include "ions.itp"
; Include topology for SDS
#include "SDS.itp"
[ system ]
; Name
Protein in water with SDS
[ molecules ]
; Compound #mols
Protein 1
SDS 2000
SOL 36173
> 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.
Mark
> 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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