[gmx-users] 转发: [gmx-user]Error by pdb2gmx

佘安奇 she_angel at yahoo.cn
Wed May 19 08:04:37 CEST 2010

Dear Yanmei Song:
I used gromacs version 3.3.1. I update ffG45a3.rtp to include my molecule. When I run pdb2gmx using my molecules with the command:
"pdb2gmx -f min_C16.pdb -o C16.pdb -p topol.top -ff G45a3"
 I got the error message:
"  Opening library file ffG45a3.rtp
  Opening library file  /user/localgromacs/share/gromacs/top/aminoacid.dat
  Reading min_C16.pdb... 
 ', 81 atomsin in water
  Opening library file  /user/localgromacs/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 1 residues with 81 atoms

    chain  #res #atoms
     1 '  '     1     81
  All occupancies are one
  Opening library file ffG45a3.atp
  Atomtype 49
  Reading residue database... (ffG45a3)
   Opening library file ffG45a3.rtp
  Using default: not generating all posible dihedrals
  Using default:excluding 3 bonded neighbors
  Using default: generating 1,4 H--H interactions
 Using default: removing impropers on same bond as a proper
>>>> Program pdb2gmx, VERSION 3.3.1
>>>> Source code file: resall.c, line: 331
>>>> Fatal error:
>>>> in .rtp file at line: " 
The molecule I added in the ffG45a3.rtp is in attached file

Thank you very much indeed.

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