I have a system in which a ligand is attached with the small peptide of the length of 8 Amino Acids. I want to perform Molecular Dynamics of this system. What procedure and software should I use for such systems?
I think that you can use Gromacs package to perform this simulation. There are many tutorials of this kind of systems. You can find it here: http://www.gromacs.org/Documentation/Tutorials
soft :
http://ambermd.org/
procedure:
http://ambermd.org/tutorials/advanced/tutorial9/
best
Hi Vinicius,
I have tried Gromacs but it failed to do it since the system is too small. The other problem associated with Gromacs is the small comprises of the Si-O-Si bonds and these bonds sometimes covalently bonded with the Pepitdes alpha carbon. And I want to perform the molecular dynamics individually without using any protein bound state.
Thanks!!
Hi Hamed,
As I mentioned in the above comment the complexity of the problem. Does Amber has anything which can resolve the issue for using polysiloxanes and peptides together and performing the molecular dynamics study. As Amber is paid software can you suggest me some other tools & Softwares to perform the same task.
Thanks!
The problems you will face will be uniform across any simulation software, so I really don't understand the statement "I have tried Gromacs but it failed to do it since the system is too small." That just doesn't make sense.
I also don't understand what you're trying to do - you say you've got some Si-O-Si species bound to alpha carbons, but then you say you want to do the simulations "without using any protein bound state." Can you please very clearly explain what you want to do?
The biggest issue is with employing a suitable force field. If you have covalent bonds between peptide moieties and a polysiloxane, you will have to introduce new bonded (and perhaps nonbonded) parameters for those interactions; it's very non-standard. That much is true of any program you use (Gromacs, Amber, NAMD, etc). None of them will easily handle your case by default. You have to extend the existing force fields to understand a suitable force field.
Hi Justin,
1. The system
The system is made of polysiloxane covalently linked with 8 amino acid linked peptide.
Si-O-Si-Ca
| |
O O
| |
Si-O-Si-Ca
Ca = C-alpha
2. Protein bound state means a big protein ( > 120 AA) along with that the system is bound to it.
So Basically I want to perform MD of such system. I can extend the system but the basic unit if we take that comprises of 1 square block made up of Si-O-Si and 4 AminoAcids. Which is very small to perform a molecular dynamics through Gromacs.
And your third paragraph exactly describes my problem to develop these force fields. So I wanted to know if there is any Software which treats the atoms of such system perform molecular dynamics for such an small system together.
I am open for all kinds of suggestions.
Thanks !!
I think that you may be interested also in LAMMPS.
There you can find an example of a peptide solved in water. Is quite easy to use.
Then, to add some Si-O-Si molecules etc, in principle, should be possible -if I remember correctly- ussing the hybrid pair style.
The size of the system is not a problem unique to any particular software; if it is too small to simulate the reason is potential violations of the minimum image convention. That's a problem with any software.
Simulations of silica and similar materials are done all the time; you'll have to figure out if any of these force fields have been derived in a manner compatible with any biomolecular force field or if they have been designed only as standalone. If the former, then you can easily implement these parameters just about anywhere. If the latter, then you'll have to do such derivation yourself.
Thanks Alberto!
I am trying to learn LAMMPS and I will try to incorporate the changes. I think this will work based on the documentation provided on the website.
Justin I think I have to modify the amber99 so that the MD of peptide can also be performed. Thanks for the help !!
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