|
|
|
Energy terms, Constraints, Restraints, and Solvation
|
|
What do you mean when you say that you gave "QECONT .eq. 0"? You should normally give values to EU, and the derivatives of your energy function to DX,DY,DZ. If your energy function is E=(X,Y,Z), then you get (DX,DY,DZ) = grad(E(X,Y,Z)) ie,
|
|
Energy terms, Constraints, Restraints, and Solvation
|
|
Thank you Lennart for your suggestions. I tried it by just making small changes in usersb. I gave "QECONT .eq. 0" then while performing installation, its giving error in usersb.f Installation command (serial only for initial test) ./install
|
|
Molecular Dynamics
|
|
Hi all, Just one question about constant pH MD: I want to perform MD under various pH values, so if CPHMD is applied, will the backbone H-bond be affected? Or to say, will the partial charge of backbone atom be altered when simulated under differe
|
|
Parameter Set Discussion
|
|
Dear Kenno, Thanks for the explanation of dihedral canceling out in the energy expression. So, in my case the CG301 center binds to three substituents apart from 120 from each other and the dihedrals are two fold. The dihedral parameters are not in
|
|
Parameter Set Discussion
|
|
Originally Posted By: AscarisAh, yes, I believe I did use ic generate to create this IC table (because of what Kenno said in his tutorial about being able to use that command to generate an IC table).To tell you the truth, my arm was twisted to put t
|
|
Parameter Set Discussion
|
|
I would have told you if I did...
|
|
Parameter Set Discussion
|
|
Just FYI, there's yet another urea model in CGenFF. I believe Alex put it together (but don't take my word for it). It might be interesting to test it along with the others.
|
|
Parameter Set Discussion
|
|
Originally Posted By: tianjThis is the same as what it is in Amber force field. That's an outrage! We have to change the CHARMM combing rules! Perhaps we might use these ones for the CHARMM Drude Polarizable FF: C. Baker et al., J. Chem. Theory Co
|
|
Parameter Set Discussion
|
|
Without the IC table: read rtf card name ... read para card name ... read sequence fg1 1 generate fg1 read coor pdb name fg1.pdb hbuild sele hydrogen end You may of course still have problems with missing parameters.
|
|
Parameter Set Discussion
|
|
Lennart- I do have x,y,z coordinates, and 3DP9 is indeed the source... I had tried skipping the IC table business earlier, had run into some problems, and—concerned that the lack of an IC table might be the source—then proceeded to attempt to make s
|
|
CHARMMing
|
|
All, I have managed to restore www.charmmtutorial.org to operation. I am still working on www.charmming.org and expect that it will take several days. The reason for this is I have been planning to upgrade www.charmming.org to the latest version of
|
|
Parameter Set Discussion
|
|
Assuming a planar molecule, consider the following-- Code:IC C6 N1 C2 N3 0. 0. 0. 0. 0.
IC N1 C2 N3 C4 0. 0. 0. 0. 0.
IC C2 N3 C4 C5 0. 0. 0. 0. 0.
IC N3 C4 C5 N7 0. 0. 180. 0. 0.
IC C4 C5
|
|
Bug Reports & Fixes
|
|
Hello I am trying to run Hamiltonian replica exchange on dialanine in vacuo with langevin dyn. In this system, as far as I can see, when a test exchange of coords is attempted, the hamiltonians are also exchanged. This is a problem since the p
|
|
Bug Reports & Fixes
|
|
Good morning: There is a parameter, ocut, that works, but is missing from the coor hbond documentation. For example, the input snippet coor hbond - select segid PROT end
|
|
Energy terms, Constraints, Restraints, and Solvation
|
|
Don't move files around, just make the changes to usersb in the directory where it is. Then issue the same installation command as was used for the original installation of CHARMM. If you need an external library file you have to modify the makefiles
|
|
Energy terms, Constraints, Restraints, and Solvation
|
|
I used my energy calculation routine in the usere subroutine. But when I run the charmm script the user energy is still zero. I set the eu to be zero. I didn't use any of these flags DX, DY,DZ, QECONT,ECONT. The routine uses a library file which I
|
|
Parameter Set Discussion
|
|
Just to be sure, since you never actually mentioned anything about this: You do not happen to have x,y,z coordinates for your molecule? Would 3DP9 be of any use? You see, if you have x,y,z coordinates this whole frustrating IC-table business in the R
|
|
Parameter Set Discussion
|
|
Hi, Kenno Thank you for your help So do you know whether there is any paper that has parameterized the selenium using CHARMM protocol?
|
|
CHARMMing
|
|
The server that runs www.charmming.org and www.charmmtutorial.org suffered a hardware failure this evening. I am working on restoring the services as quickly as possible.I will keep everyone posted in this thread. My apologies for the inconvenience!
|
|
Parameter Set Discussion
|
|
By hand it is, then. But I'm still not clear on where I can find out how to create an IC table by hand, even if it only lists dihedral terms... e.g., Quote:How does one determine what dihedrals (proper and improper) need to be listed in the IC table
|
|
Parameter Set Discussion
|
|
I recommend making the IC table by hand; to quote intcor.doc-- The main purpose for this command is to be able to easily produce an IC table for internal coordinate analysis. The simple algorithm employed here does not do a very good job of g
|
|
Parameter Set Discussion
|
|
Ah, yes, I believe I did use ic generate to create this IC table (because of what Kenno said in his tutorial about being able to use that command to generate an IC table). When you say at risk of repeating yourself, are you referring to a thread (ent
|
|
Parameter Set Discussion
|
|
It is a good thing that you will now read the paper. Perhaps you will also read the Caflisch&Karplus paper. These forums are NOT, and certainly were never intended to be, a substitute for real learning - read the primary literature, do your homew
|
|
Parameter Set Discussion
|
|
The IC table may be suspect, since IC PARAM gives an error. How did you obtain the IC table itself? What you made you decide to include so many improper dihedrals? At the risk of my repeating myself, I do not recommend using IC GENERATE for this p
|
|
Parameter Set Discussion
|
|
I should have read you paper before I asked that question. Thank you.
|
