[gmx-users] Re:[gmx-user]Error by pdb2gmx( Dallas B. Warren)

[佘安奇]

> Dear Dallas:
>    Thanks a lot for your reply.
>    But I didn't quite understand "no
> function types defined in your bonds, angles and dihedrals".
> Could you give more details? 
>    
> Angel
> 
> > 

Today's Topics:

   1. RE: [gmx-user]Error by pdb2gmx (Dallas B. Warren)
   2. Re: Virial and Pressure (Mark Abraham)
   3. add missing atom (you zou)
   4. Gromacs 3.3.3 segmentation fault on SLES10.2 x86_64    Xeon
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      architecture - Intel Compilers & Intel MKL (David van der Spoel)

Message: 1
Date: Fri, 28 May 2010 12:28:04 +1000
From: "Dallas B. Warren" <Dallas.Warren at pharm.monash.edu.au>
Subject: RE: [gmx-users] [gmx-user]Error by pdb2gmx
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID:
    <89907EA1DCFB7548A431C13A270F9DD50ABDC294 at prk-exch-01.vcp.local>
Content-Type: text/plain; charset=utf-8

You have no function types defined in your bonds, angles and dihedrals.

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at pharm.monash.edu.au
+61 3 9903 9167
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail. 

> -----Original Message-----
> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-
> bounces at gromacs.org] On Behalf Of ???
> Sent: Friday, 28 May 2010 11:58 AM
> To: gmx-users at gromacs.org
> Subject: [gmx-users] [gmx-user]Error by pdb2gmx
> 
> Dear Editors:
> I used gromacs version 4.0.7. I update ffG45a3.rtp to include my
> molecule with its rtp in the attached file DRG.txt.And the pdb file of
> my molecule is mol.txt and also attached. When I used the following
> command,there is an error! "pdb2gmx_mpi  -ff G45a3 -f  iso-C16.PDB"
> 
> Opening library file ffG45a3.rtp
> Opening library file /home/gromacs4/share/gromacs/top/aminoacids.dat
> Opening library file /home/gromacs4/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 /home/gromacs4/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 /home/gromacs4/share/gromacs/top/vdwradii.dat
> Entries in vdwradii.dat: 28
> Opening library file /home/gromacs4/share/gromacs/top/dgsolv.dat
> Entries in dgsolv.dat: 7
> Opening library file /home/gromacs4/share/gromacs/top/electroneg.dat
> Entries in electroneg.dat: 71
> Opening library file /home/gromacs4/share/gromacs/top/elements.dat
> Entries in elements.dat: 218
> Reading iso-C16.PDB...
> Read 81 atoms
> Opening library file /home/gromacs4/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 /home/gromacs4/share/gromacs/top/ffG45a3.atp
> Atomtype 1
> Reading residue database... (ffG45a3)
> Opening library file ffG45a3.rtp
> Using default: not generating all possible 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
> Residue 96
> -------------------------------------------------------
> Program pdb2gmx_mpi, VERSION 4.0.7
> Source code file: resall.c, line: 344
> 
> Fatal error:
> in .rtp file in residue DRG at line:
> 
> What's up with the resall.c in line 344?
> I hope the problem won't bother you too much!
> Thank you very much!
> 
> Angel
> 
> 
> 
>