Hello again, I am still working on gromacs sims on the side of wet lab work. In any case, I am still at the same point as almost several weeks back.
I can take my pdb file with 5 chain IDs A-C and generate a .top and .gro file, with appropriate box (which can just be pasted at the top of the file I believe) along with the .itps for each chain. I then run an energy minimization in vacuo and it works fine, converging in 800-850 steps at 0.002 ps each I then add waters, and ions (K+, Ca2+, Mg2+, Na+ and Cl-)and generate the larger 37 MB pdb file. >From this, I make_ndx , and additionally specify the residues for each chain, >plus the ions, with Ca2+ in a seperate file (Protein_A-G). Now when I do a simple EM with steep, it say converged in 10-20 cycles, with a rather large force and Potential Energy = 1.9811578e+20. When I take just the protein part of the output, I find the terminal residues from each chain try to form a bond (at 10-30 Angstroms away) with the next chein, and from there the system explodes. So, How do I force a restraint, or something in gromacs which will keep the varied chains seperate, and from trying to converge or fix a gap which does not exist in a chain. I use an index file I checked all .itp files and no bonds are specified between the terminal ends I even tried staying with a .pdb file the whole time instead of .gro, but the pdb2gmx always adds an extra 4000 atoms(out of 553257) which I can not account for, as my starting .pdb has all hydrogens, etc. Basically, I just want to run a MD between a three chain and two chain protein set to observe differences upon binding, and plot the varied energy changes, along with different pharmaceuticals, etc. to compare differences,and a visualization of the movements involved, as one of the two proteins contains a number of flexible loops, etc...thus visualizatio of movement would be very helpful in illucidation of the action of varied compounds...ANd I already now read the manual 2 x it don't say much about my problem, and the two suggestions out of the 200 posts in the e-mails say use an index file, and check your .itp files for cositency. Any help or suggestions are appriciated. Sincerely, Stephan Lloyd Watkins -- GMX.ch - Schweizer FreeMail-Dienst mit über 800.000 Mitgliedern E-Mail & mehr! Kostenlos: http://portal.gmx.net/de/go/chfreemail -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
