[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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--
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Dr. Florian Haberl
Computer-Chemie-Centrum
Universitaet Erlangen/ Nuernberg
Naegelsbachstr 25
D-91052 Erlangen
Telephone: +49(0) − 9131 − 85 26573
Mailto: florian.haberl AT chemie.uni-erlangen.de
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