In Running MD simulations of some enzymes containing phosphoserine, where can we find forcefields for phosphoserine to use with "NAMD".
Thanks,
You can use charmm patch SP2 (dianionic phosphate), found in toppar_prot_na_all.str (http://mackerell.umaryland.edu/charmm_ff.shtml) to convert any residue with an -OH group into a phospho- derivative.
NAMD gives a short tutorial (http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix-html/node24.html) on using patches found in topology files.
Try out
Paramchem
Swissparam
These online tools will provide you topology as well as parameter files.
Use CHARMM-GUI (www.charmm-gui.org) and it will prepare a topology with any patch available in CHARMM, as well as providing you with input files suitable for CHARMM, NAMD, GROMACS, etc.
I have faced the same needs for the project I currently working on. I have found a useful tutorial on YouTube for mutating a Serine to a phosphoresce using VMD. Here is the link below ("Mutating a Serine to phosphoserine in VMD). In addition, Troy Messina has a website on which you can find the powerpoint of the tutorial. The publication referenced can also be useful in first intention.
It's a good starting point however, in the following videos presented there are few things I have changed to be able to be able to smoothly run the simulation on VMD.
Otherwise there is also Vienna-PTM http://vienna-ptm.univie.ac.at
But I've never been able to figure out how it works properly, since whenever I tried to run a simulation I get a bunch of errors.
Hope this will help you.
https://www.youtube.com/watch?v=fwDYAcdc6ZQ
@Dominique:
What kind of problems did you experience with Vienna-PTM? For now, we only support GROMOS force fields 45A3 and 54A7 - but in case you need just the initial starting coordinates, it might be also useful in this case.
PS: I know, that the installation of the parameter files in GROMACS can be tricky (depending on the version, you need to place the .atp file at the proper location and such).
@Christian:
I guess this topic is kind of outdated. However, for (finally!) answering your question, the problem I ran into occurred in the very first stage: when using "pdb2gmx", this was consistently showing me an error concerning the OTX atom of some residues. By copying and pasting the phosphor-residues in the original list it partially solved the problem, since after starting over 2 or 3 times (i.e, deleting GROMACS, installing, and replacing .atp file at the proper location), nothing changed.
I have now finished my work on it, which seems to have interested many members of the jury during my PhD presentation. I would like to take it further, out of curiosity and compare the results I have obtained with NAMD, with those I can obtain with GROMACS. Maybe doing screenshots at the various stages of the process could help understanding new users how to use the PTM tool.
A problem I've consistently ran into when getting familiar with these is that manuals are written as it makes sense to everyone, which is does not necessarily do. That's why a little explanation video or even just screenshots could be very helpful.
- Badges
- Science topic