Hi, i think another problem lies here: ; Include water topology > #include "spc.itp" > ................. > > ; 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
You have defined your Protein, then the water, then ions and then SDS. But in [ molecules ] you have the order Protein - SDS - water; but these two orders must be the same. -> Delete the line, which Justin suggested und put the *#include "SDS.itp"* before the *#include "spc.itp"*, then i think all must be fine. Thomas > > > ------------------------------ > > Message: 5 > Date: Wed, 17 Jun 2009 09:11:29 -0400 > From: "Justin A. Lemkul" <jalem...@vt.edu> > Subject: Re: [gmx-users] Re: protein in SDS/water > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4a38eb81.6000...@vt.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > 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: amarabo...@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" >>> >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > -- > ======================================== > > 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 > > ======================================== > > > ------------------------------ > > _______________________________________________ > gmx-users mailing list > gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > > End of gmx-users Digest, Vol 62, Issue 90 > ***************************************** _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? 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