[gmx-users] RE:Multiple chain ID's

lloyd riggs lloyd.riggs at gmx.ch
Tue Jun 22 16:21:43 CEST 2010

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.


Stephan Lloyd Watkins
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