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

[Anna Marabotti]

Dear all,
thank you for continuous support. Here briefly what I made:

1) I deleted SDS from the first [moleculetype] section of the old .top file = doesn't work
2) I added a new [moleculetype] section after #include "ions.itp", followed by #include "SDS.itp" (just before
[ system ] and [ molecule ] sections - I think it is "after the final subsection of any other [moleculetype]
section" as Mark suggested) = doesn't work
3) In [ molecules ] section I changed the order Protein-SDS-SOL with Protein-SOL-SDS = doesn't work

I really think I did all possible combination of attempts following your last suggestions...but GROMACS still
claims that the number of coordinates in coordinate file              does not match topology and the
coordinates in .top file are 0.

I'm copying here the last .top file I produced (and that doesn't work...). I kindly ask you to refer to this
file for any further suggestions.
Anna

	;
;	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

[ 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"

[ moleculetype ]
; Name	nrexcl
SDS	3

; Include topology for SDS
#include "SDS.itp"

[ system ]
; Name
Protein in water with SDS

[ molecules ]
; Compound        #mols
Protein             1
SOL             36173
SDS	        2000

I hope 

______________________________________________
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
____________________________________________________
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