[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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