Moeed wrote:
Hello Justin,
I spent a full day to find a proper value for -d but it seems there is
no way of getting correct bond lenght and angle at the same time. With
the following commands I am getting correct bond length for the atoms
connecting two monomer units but the angle is 140. I get 110 angle only
when bond distance is much less than actual value (1.53 A). I have also
tried monomer units with 6, 8, 10 carbon atoms. For 8 and 10 cases I can
not even align carbons with the axis using princ. This proper geometry
problem seems to be a very simple thing to figure out but I have reached
no results. I would like you to provide me with a hint or suggestion...I
appreciate your help. Thanks.
There are two approaches.
1. Use a semi-correct geometry and run energy minimization to resolve any weird
bonds/angles.
2. Orient your 4-carbon unit properly :) This requires special index groups for
the structure you've generated. The 4-carbon unit is not changed when using
editconf -princ. If you use this index file:
[ special ]
1 3
[ all ]
1 2 3 4
Run:
editconf -f C4.gro -o C4_princ.gro -n index.ndx -princ
(Choose group 1 for determining the size, 0 for the orientation, and 1 for
output)
Then your structure is actually aligned perfectly with the x-axis. Using
genconf should be simple at that point. A little bit of trigonometry will help
you figure out the proper value of -d. If you still can't get that to work out,
then approach #1 may work fine.
-Justin
Great Red Owns Many ACres of Sand
4
1Eth C1 1 0.462 0.285 0.269
1Eth C2 2 0.325 0.216 0.269
1Eth C3 3 0.213 0.321 0.269
1Eth C4 4 0.075 0.255 0.269
0.53817 0.53817 0.53817
editconf -f 4C.pdb -o 4Cd-princ.gro -princ -d 0.075 -bt cubic
genconf -f 4Cd-princ.gro -o 4Cd-rep.gro -nbox 5 1 1
4Cd-rep.gro: replicated units:
Great Red Owns Many ACres of Sand
20
1Eth C1 1 0.462 0.285 0.269 0.0000 0.0000 0.0000
1Eth C2 2 0.325 0.216 0.269 0.0000 0.0000 0.0000
1Eth C3 3 0.213 0.321 0.269 0.0000 0.0000 0.0000
1Eth C4 4 0.075 0.255 0.269 0.0000 0.0000 0.0000
2Eth C1 5 1.000 0.285 0.269 0.0000 0.0000 0.0000
2Eth C2 6 0.863 0.216 0.269 0.0000 0.0000 0.0000
2Eth C3 7 0.751 0.321 0.269 0.0000 0.0000 0.0000
2Eth C4 8 0.613 0.255 0.269 0.0000 0.0000 0.0000
3Eth C1 9 1.538 0.285 0.269 0.0000 0.0000 0.0000
3Eth C2 10 1.401 0.216 0.269 0.0000 0.0000 0.0000
3Eth C3 11 1.289 0.321 0.269 0.0000 0.0000 0.0000
3Eth C4 12 1.151 0.255 0.269 0.0000 0.0000 0.0000
4Eth C1 13 2.077 0.285 0.269 0.0000 0.0000 0.0000
4Eth C2 14 1.940 0.216 0.269 0.0000 0.0000 0.0000
4Eth C3 15 1.828 0.321 0.269 0.0000 0.0000 0.0000
4Eth C4 16 1.690 0.255 0.269 0.0000 0.0000 0.0000
5Eth C1 17 2.615 0.285 0.269 0.0000 0.0000 0.0000
5Eth C2 18 2.478 0.216 0.269 0.0000 0.0000 0.0000
5Eth C3 19 2.366 0.321 0.269 0.0000 0.0000 0.0000
5Eth C4 20 2.228 0.255 0.269 0.0000 0.0000 0.0000
2.69085 0.53817 0.53817
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
