[gmx-users] Re: protein in SDS/water
Thomas Schlesier
schlesi at uni-mainz.de
Wed Jun 17 15:23:22 CEST 2009
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" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] Re: protein in SDS/water
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4A38EB81.6000508 at 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: 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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