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

[Lara Bunte]

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?


Could that be a problem in further calculations, i.e. energy minimization if there is this empty [ dihedrals ] block in the topology?


>> [ 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?

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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