[gmx-users] Re: problems running grompp with protein-ligand complex

Florian Haberl Florian.Haberl at chemie.uni-erlangen.de
Tue Dec 2 13:51:23 CET 2008


Hi,

On Tuesday, 2. December 2008, Ragnarok sdf wrote:
> Hello. I will try now to send part of my itp file and if another part
> of the file is needed I will send it if requested.
> Below are the emails that were already sent regarding my problem.
> I hope I have not caused any incovenience.
> Fabrício Bracht

You have to combine all atomtypes into one file something like

filename ff_atomtypes.itp

#define FF_ATOMTYPES

[ defaults ]
; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
1               2               yes             0.5     0.8333


[ atomtypes ]
; name        mass      charge    ptype               sigma             
epsilon

      S       0.0000  0.0000  A   3.56359e-01  1.04600e+00
    CC      0.0000  0.0000  A   3.39967e-01  3.59824e-01
    HO      0.0000  0.0000  A   0.00000e+00  0.00000e+00
    N3      0.0000  0.0000  A   3.25000e-01  7.11280e-01
all atom types from amber force field 99 and also from your ligand (check if 
parameters are ok).


delete atomtypes and defaults entry in your ligand.itp

load in your .top

#include "ff_atomtypes.itp"

#include "receptor.itp"
#include "ligand.itp"

...

greetings,

Florian


>
> " I am working with a protein-ligand complex in gromacs with ffamber99
> forcefield. I was able to generate the topology file for my ligand
> with acpypi. Was also able to insert the ligand coordinates into my
> protein's coordinate file. Was also able to generate the water box
> with genbox. The number of molecules all match, the ligand coordinates
> are still there but grompp tells me that:
> Fatal error: Found a second defaults directive, file "ligand.itp", line 5
> I've checked wikigromacs, but the solution given there, to simply
> erase the second default line does not suit me here. Once I do this, i
> mean, go to my ligand.itp file and put a ; before my default section,
> grompp does not recognize anymore that my ligand is there and gives
> out another error line.
> I would like some advice on the matter if possible.
> Thank you in advance
> Fabrício Bracht
>
> >Well, it's not like grompp is recognizing you have a ligand there
> >right now, is it? grompp doesn't reach the point where it realizes you
> >don't seem to have a ligand. It seems there's something wrong with the
> >topology. Better post ligand.itp, like Justin suggests, and also give
> >the error which occurs when you do comment out the defaults line in
> >the ligand topology.
> >
> >Cheers,
> >
> >Tsjerk "
>
> Now, the actual itp file.
>
> ; M_E.top created by acpypi on Wed Nov 26 18:00:37 2008
>
> [ defaults ]
> ; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
> 1               2               yes             0.5     0.8333
>
> [ atomtypes ]
> ;name   bond_type     mass     charge   ptype   sigma         epsilon      
> Amb o        o           0.00000  0.00000   A     2.95992e-01
> 8.78640e-01 ; 1.66  0.2100
>  c        c           0.00000  0.00000   A     3.39967e-01
> 3.59824e-01 ; 1.91  0.0860
>  oh       oh          0.00000  0.00000   A     3.06647e-01
> 8.80314e-01 ; 1.72  0.2104
>  ho       ho          0.00000  0.00000   A     0.00000e+00
> 0.00000e+00 ; 0.00  0.0000
>  c3       c3          0.00000  0.00000   A     3.39967e-01
> 4.57730e-01 ; 1.91  0.1094
>  hc       hc          0.00000  0.00000   A     2.64953e-01
> 6.56888e-02 ; 1.49  0.0157
>  c2       c2          0.00000  0.00000   A     3.39967e-01
> 3.59824e-01 ; 1.91  0.0860
>  ha       ha          0.00000  0.00000   A     2.59964e-01
> 6.27600e-02 ; 1.46  0.0150
>  ce       ce          0.00000  0.00000   A     3.39967e-01
> 3.59824e-01 ; 1.91  0.0860
>  cf       cf          0.00000  0.00000   A     3.39967e-01
> 3.59824e-01 ; 1.91  0.0860
>
> [ moleculetype ]
> ;name            nrexcl
>  M_E              3
>
> [ atoms ]
> ;   nr  type  resi  res  atom  cgnr     charge      mass       typeB   
> chargeB 1    o     1    M_E   O49    1     -0.55230     16.00000 ; qtot
> -0.552 2    c     1    M_E   C48    2      0.63200     12.01000 ; qtot
> 0.080 3   oh     1    M_E   O50    3     -0.60900     16.00000 ; qtot
> -0.529 4   ho     1    M_E   H51    4      0.44690      1.00800 ; qtot
> -0.082 5   c3     1    M_E   C45    5     -0.12590     12.01000 ; qtot
> -0.208 6   hc     1    M_E   H46    6      0.08080      1.00800 ; qtot
> -0.127 7   hc     1    M_E   H47    7      0.08110      1.00800 ; qtot
> -0.046 8   c3     1    M_E   C42    8     -0.07210     12.01000 ; qtot
> -0.118 9   hc     1    M_E   H43    9      0.06640      1.00800 ; qtot
> -0.052 10   hc     1    M_E   H44   10      0.05040      1.00800 ; qtot
> -0.002 11   c3     1    M_E   C39   11     -0.05170     12.01000 ; qtot
> -0.053 12   hc     1    M_E   H40   12      0.04490      1.00800 ; qtot
> -0.008 13   hc     1    M_E   H41   13      0.05410      1.00800 ; qtot
> 0.046 14   c2     1    M_E   C37   14     -0.16730     12.01000 ; qtot
> -0.122 15   ha     1    M_E   H38   15      0.11950      1.00800 ; qtot
> -0.002 16   c2     1    M_E   C35   16     -0.16710     12.01000 ; qtot
> -0.169 17   ha     1    M_E   H36   17      0.11730      1.00800 ; qtot
> -0.052 18   c3     1    M_E   C32   18     -0.04940     12.01000 ; qtot
> -0.101 19   hc     1    M_E   H33   19      0.07250      1.00800 ; qtot
> -0.029 20   hc     1    M_E   H34   20      0.06180      1.00800 ; qtot
> 0.033 21   c3     1    M_E    C2   21     -0.00340     12.01000 ; qtot
> 0.030 22   hc     1    M_E    H6   22      0.07250      1.00800 ; qtot
> 0.102 23   c2     1    M_E    C1   23     -0.10390     12.01000 ; qtot
> -0.002 24   ha     1    M_E    H8   24      0.14850      1.00800 ; qtot
> 0.147 25   ce     1    M_E    C5   25     -0.25360     12.01000 ; qtot
> -0.107 26   ha     1    M_E    H9   26      0.16130      1.00800 ; qtot
> 0.054 27    c     1    M_E    C4   27      0.56070     12.01000 ; qtot
> 0.615 28    o     1    M_E    O7   28     -0.52650     16.00000 ; qtot
> 0.089 29   ce     1    M_E    C3   29     -0.21970     12.01000 ; qtot
> -0.131 30   cf     1    M_E   C10   30     -0.04110     12.01000 ; qtot
> -0.172 31   ha     1    M_E   H11   31      0.14510      1.00800 ; qtot
> -0.027 32   cf     1    M_E   C12   32     -0.16880     12.01000 ; qtot
> -0.196 33   ha     1    M_E   H13   33      0.12600      1.00800 ; qtot
> -0.070 34   c2     1    M_E   C14   34     -0.12090     12.01000 ; qtot
> -0.191 35   ha     1    M_E   H15   35      0.12220      1.00800 ; qtot
> -0.069 36   c3     1    M_E   C16   36     -0.06070     12.01000 ; qtot
> -0.129 37   hc     1    M_E   H17   37      0.05610      1.00800 ; qtot
> -0.073 38   hc     1    M_E   H18   38      0.05520      1.00800 ; qtot
> -0.018 39   c3     1    M_E   C19   39     -0.07610     12.01000 ; qtot
> -0.094 40   hc     1    M_E   H20   40      0.04810      1.00800 ; qtot
> -0.046 41   hc     1    M_E   H21   41      0.03740      1.00800 ; qtot
> -0.009 42   c3     1    M_E   C22   42     -0.07850     12.01000 ; qtot
> -0.087 43   hc     1    M_E   H23   43      0.04140      1.00800 ; qtot
> -0.046 44   hc     1    M_E   H24   44      0.03920      1.00800 ; qtot
> -0.007 45   c3     1    M_E   C25   45     -0.08090     12.01000 ; qtot
> -0.088 46   hc     1    M_E   H26   46      0.03910      1.00800 ; qtot
> -0.048 47   hc     1    M_E   H27   47      0.04220      1.00800 ; qtot
> -0.006 48   c3     1    M_E   C28   48     -0.09280     12.01000 ; qtot
> -0.099 49   hc     1    M_E   H29   49      0.03180      1.00800 ; qtot
> -0.067 50   hc     1    M_E   H30   50      0.03440      1.00800 ; qtot
> -0.033 51   hc     1    M_E   H31   51      0.03280      1.00800 ; qtot
> -0.000
>
> [ bonds ]
> ;   ai     aj funct   r             k
>      3      4   1    9.7400e-02    3.0928e+05 ;    O50 - H51
> (more text not sent)
> [ pairs ]
> ;   ai     aj    funct
>      6      9      1 ;    H46 - H43
> (more text not sent)
>
> [ angles ]
> ;   ai     aj     ak    funct   theta         cth
>      2      3      4      1    1.0737e+02    4.2844e+02 ;    C48 - O50
>    - H51
> (more text not sent)
>
> [ dihedrals ] ; propers
> ; treated as RBs in GROMACS to use combine multiple AMBER torsions per
> quartet ; i   j   k   l func   C0        C1        C2        C3        C4  
>      C5 1   2   3   4   3   27.19600   -7.94960  -19.24640    0.00000
> 0.00000    0.00000 ;    O49-   C48-   O50-   H51
> (more text not sent)
>
> [ dihedrals ] ; impropers
> ; treated as propers in GROMACS to use correct AMBER analytical function
> ; i   j   k   l func  phase     kd      pn
>  16  11  14  15   1   180.00   4.60240   2 ;    C35-   C39-   C37-   H38
> (more text not sent)
>
> [ system ]
>  M_E
>
> [ molecules ]
> ; Compound        nmols
>  M_E              1
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 Dr. Florian Haberl                        
 Computer-Chemie-Centrum   
 Universitaet Erlangen/ Nuernberg
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 Mailto: florian.haberl AT chemie.uni-erlangen.de
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