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

Justin A. Lemkul jalemkul at vt.edu
Tue Jun 22 16:29:17 CEST 2010

lloyd riggs wrote:
> 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.

The box vectors are placed at the *bottom* of a .gro file.  Do be careful about 
manually setting a box.  If your coordinates are not positioned appropriately 
and have not been given sufficient solute-box space, then you might see weird 
behavior.  Instead of manually hacking the box, use editconf - that's its purpose.

> I then run an energy minimization in vacuo and it works fine, converging in
> 800-850 steps at 0.002 ps each

Just FYI, EM is run in steps, not time units.

> 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.

There is no bond formation, that's just a visualization artifact from an 
exploding system.  Is your box size sufficiently large to avoid spurious PBC 
interactions?  Where does the system start to explode?  Any LINCS warnings? 
These will point you to the part of the structure where the geometry starts to fail.


How did you produce the topology?  Did you use pdb2gmx -merge?  Did you specify 
the appropriate termini?  It sounds to me like mdrun thinks your molecules 
should be continuous peptide chains rather than separate proteins.

> 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.

That depends on your answer to my question about pdb2gmx. 
Topologically-distinct structures should not do this, and there is no way to 
enforce a restraint to work around a severely broken system.

> 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.

Then you'd better figure out what's going on - pdb2gmx doesn't just add atoms 
for fun.  Seeing your exact commands for your entire procedure and any weirdness 
in the output is the only way to diagnose this.  What you've described sounds 
like nonsense.


> 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


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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