On 24/07/2012 6:07 PM, Broadbent, Richard wrote:
An Angle constraint amounts to fixing a triangle. To do this you need to
constrain the distances between all the atoms as you know the of the bonds
6064, 6063 and 6063, 6065 and the angle between the two bonds it is a
trivial geometry problem calculate the length of the third side of the
triangle (6064,6065). However, as you are attempting to hold these atoms in
a straight line I would suggest that a type 2 virtual site might (depending
on your system) be a better idea.
Indeed, a much better idea.
Mark
Richard
On 24/07/2012 07:21, "tarak karmakar" <tarak20...@gmail.com> wrote:
Oh ! Thnaks
I saw that table, the angle_restrain option is there but not constraints .
Anyway if suppose, I fix the distance between the two terminal atoms
of the molecule, the angle will eventually be fixed at a particular
given value. Is that the logic ?
Actually I searched for this problem so many times but didn't get
proper clue; in one of those mails I saw someone has dealt with some
dummy atoms. I could not able to digest that logic.
On Tue, Jul 24, 2012 at 11:01 AM, Mark Abraham <mark.abra...@anu.edu.au>
wrote:
On 24/07/2012 3:21 PM, tarak karmakar wrote:
Dear All,
I am constraining one angle in my protein sample by incorporating " [
constraints ]" block in topology file as
[ constraints ]
; index1 index2 index3 funct angle
6064 6063 6065 1 180.0
while doing that its showing the following error
Program grompp, VERSION 4.5.5
Source code file: topdirs.c, line: 174
Fatal error:
Invalid constraints type 6065
For more information and tips for troubleshooting, please check the
GROMACS
website at http://www.gromacs.org/Documentation/Errors
As you will see in table 5.6, this is not a valid option for [constraints] -
you can only specify bonds. You will need to construct a triangle of bond
constraints.
Mark
Then I rechecked the angle block, that specific angle is there in that
angle section, part of it as follows
6039 6057 6058 1
6039 6057 6059 1
6058 6057 6059 1
6064 6063 6065 1
6067 6066 6068 1
6067 6066 6069 1
6068 6066 6069 1
6071 6070 6072 1
6071 6070 6073 1
6072 6070 6073 1
[ constraints ]
; index1 index2 index3 funct angle
6064 6063 6065 1 180.0
[ dihedrals ]
; ai aj ak al funct c0 c1
c2 c3 c4
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Only plain text messages are allowed!
* 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-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Only plain text messages are allowed!
* 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-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
