[gmx-users] Re: protein in SDS/water
Justin A. Lemkul
jalemkul at vt.edu
Wed Jun 17 15:11:29 CEST 2009
Anna Marabotti wrote:
> 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
>
Here's your problem. You've defined two molecule types in one moleculetype
directive. Look in SDS.itp - you'll likely find the moleculetype is defined
there as well.
-Justin
> [ 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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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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