[gmx-users] Re: protein in SDS/water
Justin A. Lemkul
jalemkul at vt.edu
Wed Jun 17 16:06:46 CEST 2009
Thomas Schlesier wrote:
> 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.
>
I used to think this was true, too. But it was pointed out to me that the order
of the #includes does not matter, only the order in which the species appear in
the [ molecules ] section.
-Justin
> 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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>> End of gmx-users Digest, Vol 62, Issue 90
>> *****************************************
>
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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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