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

[Richard Broadbent]

On Tue, 2012-05-15 at 15:43 +0100, 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?
> 
Not that I'm aware of, and gromacs is designed to allow 2 dihedral
blocks, I'd suggest you simply remove the block you do not want.
Although you should be very sure that is what you want to do! 
> 
> Could that be a problem in further calculations, i.e. energy minimization if there is this empty [ dihedrals ] block in the topology?
> 
Not that I'm aware of; however, you should know that those missing
parameters will be filled in with the dihedrals from the
[ dihedral_types ] section above them in the .top file (this will most
likely be in a #included file). 
> 
> >> [ 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?
> 
I don't know them but they will be in the CHARMM27.ff/amioacids.rtp file
which should be in $GMXDATA/gromacs/top/

Richard 
> Thanks
> 
> Greetings
> 
> Lara
> 
> 
> 
> 
> 
> 
> 
> ----- Ursprüngliche Message -----
> Von: Mark Abraham <Mark.Abraham at anu.edu.au>
> An: Discussion list for GROMACS users <gmx-users at gromacs.org>
> CC: 
> Gesendet: 12:57 Dienstag, 15.Mai 2012
> Betreff: Re: [gmx-users] Two [ dihedrals ] sections in topology
> 
> On 15/05/2012 8:47 PM, Lara Bunte wrote:
> > Hi
> >
> > After pdb2gmx I have two [ dihedrals ] sections in my topology. The first block is empty, the second block is correct with my parameters.
> >
> >
> > An an example:
> >
> >
> > First block:
> > [ dihedrals ]
> > ;  ai    aj    ak    al funct            c0            c1            c2            c3            c4            c5
> >      2     1    19     8     5
> >      6     8     9    10     5
> >
> >
> > Second block:
> > [ dihedrals ]
> > ;  ai    aj    ak    al funct            c0            c1            c2            c3
> >      1     8     6     4     5    180   100
> >      1     2     4     5     5    180   100
> >
> >
> > What could be the reason for this? What do I have to change in my force field folder (CHARMM27) to fix this?
> 
> Two blocks of dihedrals are normal output for pdb2gmx - one for proper 
> and one for improper dihedrals.
> 
> >
> > In my .rtp file in the force field folder I have only this section for dihedrals
> >
> > [ impropers ]
> > O4     N1      C2       N3     180   100
> > N1     C2      N3       H3     180   100
> 
> This produces your second block of type 5 dihedrals, given what you have 
> said below.
> 
> >
> >
> > I declared my [ bondedtypes ] as the following:
> >
> > [ 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.
> 
> Mark
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