bob dole wrote:
Hello,
I have conducted several runs in which I pull one peptide away from
another; however, the peptide being pulled gets visually “stretched” out
when viewing the trajectory in VMD and DSSP confirms this. I came across
this recent post
(http://lists.gromacs.org/pipermail/gmx-users/2011-September/064621.html)
in which it was recommended to apply distance restraints and use
particle decomposition to solve the stretching problem.
I tried this, but grompp keeps throwing this error:
-------------------------------------------------------
Program grompp, VERSION 4.5.4
Source code file: toppush.c, line: 1526
Fatal error:
[ file disres.itp, line 5 ]:
Atom index (1583) in distance_restraints out of bounds (1-1578).
This probably means that you have inserted topology section
"distance_restraints"
in a part belonging to a different molecule than you intended to.
In that case move the "distance_restraints" section to the right molecule.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
Here’s the workflow I used:
1) Making indices
make_ndx –f NPT.gro –o index.ndx
> a 1-789
> 19 a_1-1578 : 789 atoms
> a 790-1578
> 20 a_1579-3156: 789 atoms
> name 19 Chain_A
> name 20 Chain_B
> 20 & a CA
Copied index group 20 'a_1579-3156'
Found 208 atoms with name CA
Merged two groups with AND: 1578 208 -> 104
21 a_1579-3156_&_CA : 104 atoms
Making the distance restraint
genrestr -f NPT.gro -o disres.itp -disre -n index.ndx
Select a group: 21
3) Then I added:
#ifdef POSRES_B
#include "disres.itp"
#endif
after the include statement for the position restraint file to the *.itp
file for the peptide being pulled
4) Next I added “disre = simple” and “define -DDISRES to the MDP setting
That #define statement won't work. If your disres.itp is under the control of
"POSRES_B" then "DISRES" will have no effect.
5) Next, I run grompp as follows (after which I get the aforementioned
warning):
grompp -f PULL.mdp -c NPT.gro -p topol.top -n index.ndx -t NPTpbc.trr -o
PULL.tpr
Initially I use pdb2gmx -chainsep to tell GMX not to treat the two
peptides as 1 molecule, and when the topologies are written for the
peptides, they both start at atom 1. It's obvious that the out of bounds
warning is due to an atom numbering issue (grompp doesn't realize that
atom 1583 = atom 5 when you renumber the second peptide starting at 1),
but I've drawn a blank as to how to work around this.
Atom numbering is done on a per-moleculetype basis. To be absolutely sure, you
can have pdb2gmx renumber with -renum, or genconf -renumber before generating
the distance restraint file.
-Justin
Any suggestions will be greatly appreciated
Thanks!
--
========================================
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
========================================
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