[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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