[gmx-users] Re: Error by pdb2gmx

[wuxiao]

Dear Song,

  I guess that the problem you encountered does not matter the GROMACS. On contrary, I think that you must have edited the pdb file and made mistakes of the file format so that pdb2gmx can not tell it correctly. I wish this information can help you to deal with the problem.

 

xiaowu

 

Yanmei Song wrote:
> Dear Justin:
> 
> Thank you so much for your help earlier. I updated my GROMACS to
> 4.0.4. When I run pdb2gmx using the following two files. I still got
> the similar error message:
> 
> Opening library file ffoplsaa.rtp
> Opening library file /packages/gromacs-4.0.4/share/gromacs/top/aminoacids.dat
> Opening library file /packages/gromacs-4.0.4/share/gromacs/top/aminoacids.dat
> WARNING: masses will be determined based on residue and atom names,
> this can deviate from the real mass of the atom type
> Opening library file /packages/gromacs-4.0.4/share/gromacs/top/atommass.dat
> Entries in atommass.dat: 178
> WARNING: vdwradii will be determined based on residue and atom names,
> this can deviate from the real mass of the atom type
> Opening library file /packages/gromacs-4.0.4/share/gromacs/top/vdwradii.dat
> Entries in vdwradii.dat: 28
> Opening library file /packages/gromacs-4.0.4/share/gromacs/top/dgsolv.dat
> Entries in dgsolv.dat: 7
> Opening library file /packages/gromacs-4.0.4/share/gromacs/top/electroneg.dat
> Entries in electroneg.dat: 71
> Opening library file /packages/gromacs-4.0.4/share/gromacs/top/elements.dat
> Entries in elements.dat: 218
> Reading pdms2.pdb...
> Read 13 atoms
> Opening library file /packages/gromacs-4.0.4/share/gromacs/top/xlateat.dat
> 26 out of 26 lines of xlateat.dat converted succesfully
> Analyzing pdb file
> There are 1 chains and 0 blocks of water and 3 residues with 13 atoms
> 
> chain #res #atoms
> 1 ' ' 3 13
> 
> All occupancies are one
> Opening library file /packages/gromacs-4.0.4/share/gromacs/top/ffoplsaa.atp
> Atomtype 1
> Reading residue database... (ffoplsaa)
> Opening library file ffoplsaa.rtp
> 
> -------------------------------------------------------
> Program pdb2gmx_d, VERSION 4.0.4
> Source code file: resall.c, line: 279
> 
> Fatal error:
> in .rtp file at line:
> 
> 
> -------------------------------------------------------
> 
> My new residue added to ffoplass.rtp is:
> [ PDM ]
> ; designation arbitrary, C1 and C2 is -CH3
> [ atoms ]
> SI1 SI 0.300 1
> C1 opls_069 0.000 1
> C2 opls_069 0.000 1
> O1 opls_108 -0.300 1
> 
> [ bonds ]
> SI1 -O1
> SI1 C1
> SI1 C2
> SI1 O1
> O1 +SI1
> 
> 
> ; Terminal PDMS residue ("beginning" of chain)
> ; designation arbitrary, C1 C2 and C3 is -CH3
> [ PDMB ]
> [ atoms ]
> C1 opls_069 0.000 1
> SI1 SI 0.300 1
> C2 opls_069 0.000 1
> C3 opls_069 0.000 1
> O1 opls_108 -0.300 1
> 
> [ bonds ]
> SI1 C1
> SI1 C2
> SI1 C3
> SI1 O1
> O1 +SI1
> 
> 
> ; Terminal PE residue ("end" of chain)
> ; designation arbitrary, C1 C2 and C3 is -CH3
> 
> [ PDME ]
> [ atoms ]
> SI1 SI 0.000 1
> C1 opls_069 0.000 1
> C2 opls_069 0.000 1
> C3 opls_069 0.000 1
> 
> [ bonds ]
> SI1 -O1
> SI1 C1
> SI1 C2
> SI1 C3
> 
> PDB file:
> 
> ATOM 1 SI1 PDMB 1 8.995 -3.779 -2.091 1.00 0.00
> ATOM 2 C1 PDMB 1 10.682 -3.453 -2.828 1.00 0.00
> ATOM 3 C2 PDMB 1 8.020 -2.184 -2.039 1.00 0.00
> ATOM 4 O1 PDMB 1 8.142 -4.958 -3.082 1.00 0.00
> ATOM 5 C3 PDMB 1 9.192 -4.446 -0.356 1.00 0.00
> ATOM 6 SI1 PDM 2 6.710 -5.932 -3.395 1.00 0.00
> ATOM 7 O1 PDM 2 6.960 -6.886 -4.852 1.00 0.00
> ATOM 8 C1 PDM 2 6.403 -7.074 -1.946 1.00 0.00
> ATOM 9 C2 PDM 2 5.231 -4.812 -3.628 1.00 0.00
> ATOM 10 SI1 PDME 3 6.370 -8.062 -6.022 1.00 0.00
> ATOM 11 C1 PDME 3 7.679 -8.351 -7.325 1.00 0.00
> ATOM 12 C2 PDME 3 5.990 -9.673 -5.153 1.00 0.00
> ATOM 13 C3 PDME 3 4.816 -7.411 -6.834 1.00 0.00
> TER
> 
> Thanks a lot!
> 
> 
> 
> 
> 


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