[gmx-users] Re: protein in SDS/water

Anna Marabotti anna.marabotti at isa.cnr.it
Wed Jun 17 15:05:55 CEST 2009


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

[ 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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