[gmx-users] about pdb2gmx and topology database

[David van der Spoel]

On Wed, 2002-12-11 at 09:33, nanyu101 wrote:
> Hi,
>   My molecule is polyester.I have created block topology as below:
>
> Reading residue database... (ffgmx)
> Opening library file /usr/local/gromacs/share/top/ffgmx.rtp

it seems pdb2gmx is reading the default rtp file. Is this the one you
modified? I would recommend that you put your stuff in a file called
ffgmx.rtp in your working directory. pdb2gmx will tell you which one it
is reading.

> Using default value - not generating all possible dihedrals
> Using default value - excluding 3 bonded neighbors
> Residue 97
> Sorting it all out...
> Opening library file /usr/local/gromacs/share/top/ffgmx.hdb
> Opening library file /usr/local/gromacs/share/top/ffgmx-n.tdb
> Opening library file /usr/local/gromacs/share/top/ffgmx-c.tdb
> 
> Back Off! I just backed up pp.top to ./#pp.top.2#
> Processing chain 1 (768 atoms, 128 residues)
> Opening library file /usr/local/gromacs/share/top/specbond.dat
> 5 out of 5 lines of specbond.dat converted succesfully
> There are 0 donors and 0 acceptors
> There are 0 hydrogen bonds
> Fatal error: Residue 'EST' not found in residue topology database
> 
> 
> 
> Would somebody give me some help?Thanks a lot.
> 
> Best,
> Xianhui 
> 
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