[gmx-users] Two [ dihedrals ] sections in topology

Lara Bunte lara.bunte at yahoo.de
Thu May 17 16:48:51 CEST 2012


grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr

gives me errors like

ERROR 1 [file topol.top, line 233]:
  No default Improper Dih. types

and so on. This line 233 is the starting of my empty [ dihedrals ] block. I erase it by hand out of my topology, so that only the correct [ dihedrals ] out of the .rtp and ffbonded.itp file are in the topology. After this grompp works without error and even without any warning. 

So the question how to force pdb2gmx to use only my [ dihedrals ] block is important for me, because I don't like to erase it always by hand out of the topol.top file.


----- Ursprüngliche Message -----
Von: Mark Abraham <Mark.Abraham at anu.edu.au>
An: Discussion list for GROMACS users <gmx-users at gromacs.org>
Gesendet: 2:35 Mittwoch, 16.Mai 2012
Betreff: Re: [gmx-users] Two [ dihedrals ] sections in topology

On 16/05/2012 4:53 AM, Lara Bunte wrote:
> Hi
>> Is there some reason to believe you should not have dihedrals?  That doesn't
>> make much physical sense.
> I want and have dihedrals in my topology. I don't want an additional empty dihedrals block in the topology. In my force field I gave impropers.

An empty block of dihedrals doesn't hurt, but you don't have one of 
these. A block of dihedrals lacking parameters gets those parameters 
looked up from ffbonded.itp. You likely can't have only improper 
dihedrals and expect any resemblance to the behaviour of the CHARMM27 

It sounds to me like you're trying to do something that might not be 
worth attempting, but this thread hasn't revealed your objective. 
There's no point moving deckchairs on the Titanic if there's icebergs 
all around.


> Greetings
> ----- Ursprüngliche Message -----
> Von: Justin A. Lemkul<jalemkul at vt.edu>
> An: Lara Bunte<lara.bunte at yahoo.de>; Discussion list for GROMACS users<gmx-users at gromacs.org>
> CC:
> Gesendet: 17:02 Dienstag, 15.Mai 2012
> Betreff: Re: [gmx-users] Two [ dihedrals ] sections in topology
> On 5/15/12 10:43 AM, Lara Bunte wrote:
>> Hi
>> You wrote:
>>> Two blocks of dihedrals are normal output for pdb2gmx - one for proper
>>> and one for improper dihedrals.
>> Is there a way to force pdb2gmx that there is only my block with improper dihedrals in the topology?
> Normally pdb2gmx will generate proper dihedrals based on bonded connectivity.
> Is there some reason to believe you should not have dihedrals?  That doesn't
> make much physical sense.
>> Could that be a problem in further calculations, i.e. energy minimization if there is this empty [ dihedrals ] block in the topology?
> What you've been defining as "empty" is not necessarily so.  The fact that
> parameters are not explicitly printed is not inherently indicative of a problem,
> since the parameters are looked up from ffbonded.itp and not necessarily
> recapitulated in the topology.  If you get fatal errors about missing
> parameters, that's a separate issue.
>>>> [ bondedtypes ]
>>>> ; bonds  angles  dihedrals  impropers
>>>>           1       1          5          5
>>> Those are angle, dihedral and improper function types that are abnormal
>>> for CHARMM27. Using these in your .rtp means that you are no longer
>>> using CHARMM27. It might be reasonable for you to do this, but you need
>>> to be absolutely sure why. Importing a topology from another force field
>>> is not an acceptable reason.
>> What would be the correct numbers in the [ bondedtypes ] for using CHARMM27 force field?
> Look in charmm27.ff/aminoacids.rtp.
> -Justin

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