[gmx-users] Two [ dihedrals ] sections in topology
lara.bunte at yahoo.de
Tue May 15 16:43:05 CEST 2012
>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?
----- Ursprüngliche Message -----
Von: Mark Abraham <Mark.Abraham at anu.edu.au>
An: Discussion list for GROMACS users <gmx-users at gromacs.org>
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:
> 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
> 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.
gmx-users mailing list gmx-users at gromacs.org
Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
More information about the gromacs.org_gmx-users