[gmx-users] Re: chain ids (2)

Mark Abraham mark.abraham at anu.edu.au
Wed Jun 23 09:17:43 CEST 2010

----- Original Message -----
From: lloyd riggs <lloyd.riggs at gmx.ch>
Date: Wednesday, June 23, 2010 15:49
Subject: [gmx-users] Re: chain ids (2)
To: gmx-users at gromacs.org

> Dear All, 
> I am re-posting with some replies to my first message.
> > the cell demensions for .gro files are at the bottomn, 
> you know, you right.  There at the top for .pdb file, and 
> it is just a unit cell, and not very trivial to center 
> graphically. 

Sure, that's one thing editconf is good for.

> And when you answere somones question like below, you should 
> read what they stated first.
> >> 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 used the term step even?  Correcting every little thing 
> to the point of overdoing it makes people not want to talk to 
> you, especially when it does not solve or answere the 
> problem.  I'm not your dad, you don't have to prove 
> something to me, I know how well you know the software.

When someone asks for help, and appears to demonstrate that they've missed an important point (i.e. that time does not elapse during EM), then a helpful tip might save them lot of pain at some stage. The person giving the tip isn't trying to put anyone down - they're giving their time for free in order to be helpful. Criticising the person giving the tip is a great way to dissuade others from helping you, too. :-)
> In any case, It is obvious my problem is the system blowing up, 
> visually it is only the terminal residues from each chain, and 
> from runs such as lincs warnings, it is the same atoms in these 
> terminal residues, which are the problem.
> Basically, gromacs, as I said, can not keep the chain ids, even 
> when I use an index file, and beforehand, yes I checked all the 
> .itp, .ndx etc to make sure atoms are all properly coordinated.

The chain IDs are irrelevant to GROMACS once pdb2gmx finishes. The information encoded by differences in chain ID have been incorporated into the [molecules] section.
> The extra atoms, I can acount for a couple, such as the extra 
> hydrogen at terminal end, and yes even the interactive use of 
> pdb2gmx as a starting point for the topology still gives 
> problems. 
> Timing wise, it seems to break down when I add waters, when I 
> run this alone, it starts to explode.  I have tried step by 
> step making of .top files as well, and re-adding chain IDs after 
> a crash, etc...or just following a step by step proceedure from 
> scrath again several times.  As I had stated, if the system 
> only has the 5 proteins, and no solvent, it has no problem, but 
> then this is usually the first run after switching from a pdb to 
> .gro file, whith the .pdb generating the .top with it's 
> origional chain IDs.
> SAnd like I said, any helpful suggestions are appriciated.

Justin gave you several - such as providing us with actual pdb2gmx command lines. I agree with his guess that you've managed to produce a topology where what you intend to be your end-of-chain terminal residues are in fact bound in an inter-chain fashion. We can't do more than guess in the absence of actual evidence, however.

I do suggest starting afresh in a clean working directory with a version of the problem that is as simple as possible  :-)


> 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.
> http://www.gromacs.org/Documentation/Terminology/Blowing_Up
> 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.
> -Justin
> > 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
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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