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 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. Any suggestions will be greatly appreciated Thanks!
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