Hi,
I have done energy minimization for my particular structure using gromacs ,after energy minimization what i found is that in my structure one bond is broken, it's a cyclic peptide constitutes with six amino acids,
i set standard bond distance and bond angels for the structure then still why it breaks ?
What i can do now?
Regards
Nikhil
How do you minimize your structure? How you create the cyclic peptide, from scratch?
If a particualar bond breaks you can fix it(i.e. provide an artificially higher energy). Also, you need to check that during the minimization process the chirality of all the amino acids is conserved.
I always minimize using: 1) Steepest descent method and then 2) Newton method.
i created cylcic peptide using chemcraft software and minimized using gromacs standard procedure,defined em.mdp pr.mdp and run.mdp
only a particular bond is breaking all the time
If you knwo which bond is breaking, fix the distance in the model, that would preserve the distance during the minimization process.
I am familiar with InsightII and Yasara, it can be done easily, Not sure about how is done in Gromacs. Usually you assing a high potential to that particualr bond.
Actually InsightII is paid version right? i downloaded YASARA but i couldn't make the cyclic peptide in that,i made structure in checraft after that done many things manually.
ok i will try to do that by fixing that particular bond distance.
Bonds don't break or form in MM calculations. If your structure is distorting, you have a topology problem. You need not only the bond, but angles, dihedrals, and any impropers the force field may use, also in conjunction with proper tricks in pdb2gmx to generate the initial (broken) topology that needs to be hacked.
Hi Justin,
My structure atoms are already defined in topology ,im using CHARMM27 forcefield ,it is amino acids (Six in numbers) so is there any problem with forcefield?
The force field is not the problem. Either the topology is incorrect or the coordinates clash such that a strained geometry is produced.
- Badges
- Science topic