[gmx-users] error after new addition of molecule

Thu Aug 18 09:50:54 CEST 2005

Hi Rahul,

For one thing, I don't think you want to have all of the molecule to form 
one charge group. However, the error occurs, because there are no proper 
definitions for the bonds, angles and dihedrals. Have a look at the other 
residues in the .rtp file. Following the atom names defining the 
bond/angle/dihedral is a code for the parameters (gb_*,ga_*,gd_*) which 
refers to parameters in ff*bon.itp.

By the way, if you have a polyethylene, you should be able to define just 
one ethylene and use pdb2gmx to build the chain.

Hope it helps,

Tsjerk

On 8/17/05, Rahul Karyappa <r.karyappa at ncl.res.in> wrote:
> 
> Thank you for your lind reply. Your information worked and I am able to 
> run pdb2gmx command. But when I ran grompp command it geve me following 
> error:
> 
> processing topology...
> Generated 1284 of the 1485 non-bonded parameter combinations
> WARNING 1 [file "topol1.top", line 54]:
> No default Bond types, using zeroes
> WARNING 2 [file "topol1.top", line 55]:
> No default Bond types, using zeroes
> WARNING 3 [file "topol1.top", line 56]:
> No default Bond types, using zeroes
> WARNING 4 [file "topol1.top", line 57]:
> No default Bond types, using zeroes
> WARNING 5 [file "topol1.top", line 58]:
> No default Bond types, using zeroes
> WARNING 6 [file "topol1.top", line 59]:
> No default Bond types, using zeroes
> WARNING 7 [file "topol1.top", line 60]:
> No default Bond types, using zeroes
> WARNING 8 [file "topol1.top", line 61]:
> No default Bond types, using zeroes
> WARNING 9 [file "topol1.top", line 62]:
> No default Bond types, using zeroes
> WARNING 10 [file "topol1.top", line 76]:
> No default Angle types, using zeroes
> Cleaning up temporary file gromppHDlOEd
> Fatal error: Too many warnings, grompp terminated
> 
> Generated .top file looks like as follows:
> 
> ; File 'topol1.top' was generated
> ; By user: root (0)
> ; On host: fox
> ; At date: Wed Aug 17 17:18:57 2005
> ;
> ; This is your topology file
> ; "Stop Drinking My Beer !" (The Amps)
> ;
> ; Include forcefield parameters
> #include "ffgmx.itp"
> 
> [ moleculetype ]
> ; Name nrexcl
> Protein 3
> 
> [ atoms ]
> ; nr type resnr residue atom cgnr charge mass typeB chargeB massB
> 1 C 1 PE CAA 1 -0.2913 12.011 ; qtot -0.2913
> 2 H 1 PE HAA1 1 0 1.008 ; qtot -0.2913
> 3 H 1 PE HAA2 1 0.145 1.008 ; qtot -0.1463
> 4 H 1 PE HAA3 1 0.145 1.008 ; qtot -0.0013
> 5 C 1 PE CAB 1 -0.2888 12.011 ; qtot -0.2901
> 6 H 1 PE HAB1 1 0.1451 1.008 ; qtot -0.145
> 7 H 1 PE HAB2 1 0.1451 1.008 ; qtot 9.999e-05
> 8 C 1 PE CAC 1 -0.2913 12.011 ; qtot -0.2912
> 9 H 1 PE HAC1 1 0.145 1.008 ; qtot -0.1462
> 10 H 1 PE HAC2 1 0.145 1.008 ; qtot -0.0012
> 11 C 1 PE CAD 1 -0.2888 12.011 ; qtot -0.29
> 12 H 1 PE HAD1 1 0.1451 1.008 ; qtot -0.1449
> 13 H 1 PE HAD2 1 0.1451 1.008 ; qtot 0.0002
> 14 C 1 PE CAE 1 -0.2913 12.011 ; qtot -0.2911
> 15 H 1 PE HAE1 1 0.145 1.008 ; qtot -0.1461
> 16 H 1 PE HAE2 1 0.145 1.008 ; qtot -0.0011
> 17 C 1 PE CAF 1 -0.2888 12.011 ; qtot -0.2899
> 18 H 1 PE HAF1 1 0.1451 1.008 ; qtot -0.1448
> 19 H 1 PE HAF2 1 0.1451 1.008 ; qtot 0.0003
> 20 C 1 PE CAG 1 -0.2913 12.011 ; qtot -0.291
> 21 H 1 PE HAG1 1 0.145 1.008 ; qtot -0.146
> 22 H 1 PE HAG2 1 0.145 1.008 ; qtot -0.001
> 23 C 1 PE CAH 1 -0.2888 12.011 ; qtot -0.2898
> 24 H 1 PE HAH1 1 0.1451 1.008 ; qtot -0.1447
> 25 H 1 PE HAH2 1 0.1451 1.008 ; qtot 0.0003999
> 26 C 1 PE CAI 1 -0.2913 12.011 ; qtot -0.2909
> 27 H 1 PE HAI1 1 0.145 1.008 ; qtot -0.1459
> 28 H 1 PE HAI2 1 0.145 1.008 ; qtot -0.0009001
> 29 C 1 PE CAJ 1 -0.2888 12.011 ; qtot -0.2897
> 30 H 1 PE HAJ1 1 0 1.008 ; qtot -0.2897
> 31 H 1 PE HAJ2 1 0.1451 1.008 ; qtot -0.1446
> 32 H 1 PE HAJ3 1 0.1451 1.008 ; qtot 0.0004999
> 
> [ bonds ]
> ; ai aj funct c0 c1 c2 c3
> 1 5 1 
> 5 8 1 
> 8 11 1 
> 11 14 1 
> 14 17 1 
> 17 20 1 
> 20 23 1 
> 23 26 1 
> 26 29 1 
> 
> [ pairs ]
> ; ai aj funct c0 c1 c2 c3
> 1 11 1 
> 5 14 1 
> 8 17 1 
> 11 20 1 
> 14 23 1 
> 17 26 1 
> 20 29 1 
> 
> [ angles ]
> ; ai aj ak funct c0 c1 c2 c3
> 1 5 8 1 
> 5 8 11 1 
> 8 11 14 1 
> 11 14 17 1 
> 14 17 20 1 
> 17 20 23 1 
> 20 23 26 1 
> 23 26 29 1 
> 
> [ dihedrals ]
> ; ai aj ak al funct c0 c1 c2 c3 c4 c5
> 1 5 8 11 1 
> 5 8 11 14 1 
> 8 11 14 17 1 
> 11 14 17 20 1 
> 14 17 20 23 1 
> 17 20 23 26 1 
> 20 23 26 29 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"
> 
> [ system ]
> ; Name
> Protein
> 
> [ molecules ]
> ; Compound #mols
> Protein 1
> 
> Please suggest for this. Thanking you once again.
> 
> Rahul karyappa
> NCL, Pune
> India
> 
> 
> *-- Original Message --*
> From: David van der Spoel <spoel at xray.bmc.uu.se>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Date: Wed, 17 Aug 2005 11:53:18 +0200
> Subject: Re: [gmx-users] error after new addition of molecule
> 
> On Wed, 2005-08-17 at 14:56 +0530, Rahul Karyappa wrote:
> > Dear all,
> > I wanted to add a new molecule in the forcefield database. For a
> > trial I took a 10 repeat unit chain of Polyethylene. So I added it to
> > the residue database and also in the aminoacids.dat file. When I ran
> > pdb2gmx command to generate .gro and .top file but it gave me
> > following error:
> > 
> > Fatal error: atom N not found in residue 1PE while combining tdb and
> > rtp
> > 
> > How should I proceed next? Can anyone have suggestions for this error?
> pdb2gmx -ter
> select none for termini
> 
> > Thanking you all.
> > 
> > Rahul Karyappa
> > NCL, Pune
> > India
> > 
> > 
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> -- 
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596, 75124 Uppsala, Sweden
> phone: 46 18 471 4205 fax: 46 18 511 755
> spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel<http://xray.bmc.uu.se/%7Espoel>
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