[gmx-developers] Problem with dihedral restraint in gromacs 4.6

[Landry Charlier]

May be with an example it will be better. If i would like, to  
constraint the dihedral angle of the ILE sidechain to 0°, I will write  
in the topol file:
[ dihedral_restraints]
  ;ai       aj       ak       al  funct  phi  dphi
  id_CG2   id_CB   id_CG1   id_CD   1     0     0
with the good id for each atom


In the mdp file, i put the lines
dihre           = yes
dihre_fc        = 2000
dihre_tau       = 0.0

During the grompp command line, I have the message :
-------------------------------------------------------
Program grompp, VERSION 4.6
Source code file: /usr/local/gromacs-4.6/src/kernel/toppush.c, line: 1914

Fatal error:
Incorrect number of parameters - found 2, expected 3 or 6 for Dih. Rest..
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

grompp waits a third parameter but the manual p 133 says that only 2  
parameters (phi & dphi) are required.

So, how can I put dihedral restraints?

Landraille






Quoting Mark Abraham <mark.j.abraham at gmail.com>:

> What are the lines that are giving problems in 4.6?
>
> Mark
>
> On Thu, Feb 7, 2013 at 3:39 PM, Landry Charlier <
> landry.charlier at univ-montp1.fr> wrote:
>
>> Hello,
>>
>> From the manual page 133, the dihedral restraints want 4 atoms, funct=1,
>> and 2 parameters (phi & dphi), i.e  ai   aj    ak    al  funct  phi  dphi
>> But when I start grompp, I have the error message "Incorrect number of
>> parameters - found 2, expected 3 or 6 for Dih. Rest.."
>> Is it a bug or dihedral restraints want a third parameter? which one, it's
>> not pointed out neither in the manual nor in the webpage (
>> http://www.gromacs.org/**Documentation/How-tos/**Dihedral_Restraints<http://www.gromacs.org/Documentation/How-tos/Dihedral_Restraints>
>> )
>>
>> When I try with the dihedral restraints format of gromacs version 4.5.4 -
>> i.e   ai   aj    ak    al  type  label  phi  dphi  kfac  power
>> I have the same error message.
>> Incorrect number of parameters - found 5, expected 3 or 6 for Dih. Rest
>>
>>
>> It seems that grommp wants too many parameters. Indeed, it wants 3 or 6
>> parameters whereas the correct format for gromacs4.6 needs 2 parameters and
>> the gromacs4.5.4 format needs 5 parameters.
>>
>> Thank you
>>
>> Landraille
>>
>>
>>
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>