----- Original Message ----- From: lloyd riggs <lloyd.ri...@gmx.ch> Date: Wednesday, June 30, 2010 21:55 Subject: [gmx-users] Re:Chain terminus To: gmx-users@gromacs.org
> > Dear All, > > I had posted here a week or so ago, but fixed my problem, and > wanted to post it, and ask if somone has a better method for this: > > Basically, I have 5 different proteins A-E in a pdb file. > > I can generate a toplogy initially with pdb2gmx automated, which > places the NH3 and COO- terminus. > > The resulting .gro file looses the chain ID's. This > initial .gro and .top file works for runs (MD or EM). > > I then add a box and waters, and the genbox has a built in code > for changing the .top file to match the water, which also keeps > the terminal ends properly. These files work for runs (MD > and EM) > > Now, then I add Ions (Na, K, Mg, Ca, Cl). The .top file > however is not updated with genion. The resulting .pdb or genion -p should do all this for you. I imagine decent tutorial material points this out... > .gro output still has no chain ID's, and there is a change in Correct, because GROMACS doesn't care about them because it makes no post-pdb2gmx use of them. > the number/type of atoms so a new .top has to be > generated. If I use either of the new .gro or .pdb files, No, you only need a modified .top. It's straightforward to make sure that you have #include "ions.itp" and then to edit the [molecules] section. Compare your before-and-after .top files with the diff tool to see what I mean. > the terminal ends are not maintained, nor can pdb2gmx recognize > the terminus in the interactive session without chain IDS, and > the resulting .top files leed to MD and EM runs crashing, or not > even initiallizing. > > To get around this, I write out a .pdb, cut and paste the > protein portion only and add back the chain IDs, which allows > interactive assignment of the terminuses. This is however > time consuming, as it has to be done each time for each ion. > > I woundered if anyone knows how to do this more efficienttly, > like the genbox or anothe way? genion -p or a few minutes with your .top file and a text editor post-genion would have sufficed. > Also, I probably would have not figured this out so fast without > the replies I had, mostly. If you'd told us the problem was in producing a post-genion .top, then you might have been told about genion -p straight away. I don't think I ever understood why (you thought) you needed chain IDs - that could have been my oversight, but I certainly wasn't motivated to delve into your mind to find out why you wanted them. This is a good lesson in not presupposing the form of the answer to a problem when asking for help :-) Describe the real problem, not only your secondary problems with your solution approach. The "How to ask questions the smart way" website makes this advice too! Mark
-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
