[gmx-users] grompp error with distance restraints

[Justin A. Lemkul]

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!
> 
> 
> 
> 
> 

-- 
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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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