Hi,<br><br><br>The atoms are separated by 12 A (1.2<br>> nm). The atoms I restrained are 1703 & 1712 (6151 & 6160 atoms are also<br>> from the same residues). These are the residues that looks as if they<br>> are no bonds between them. ( residues alone, peptide bond alone and the<br>> rest of the protein).<br><br>How is it that atoms that are 900 indices apart are in the same residues. I<br>don't understand. Do you mean that all four of these atoms are in the same<br>residue? Then they definitely aren't amino acids! Are these two separate<br>residues bridged by a distance restraint, that you are considering one residue?<br> Is there some bond defined in the topology between *any* of these atoms?<br><br>My protein has 5 chains. 1703 & 1712 are the numbers from chainC.itp file. This includes the distance restraints -<br><br>#ifdef DDISRES<br>[ distance_restraints ]<br>;ai aj type index type' low up1 up2 fac<br>1703 1712 1 0 1 1.15 1.20 1.25 1.0<br>#endif<br><br>6151 & 6160 atoms are the numbers from .gro file reported by the .job file. 6151 is N of residue 584 and 1703 is CA of the same redsidue. Residue 584 & 585 are placed have 14 residues missing between them. 6160 is N of residue 585 & 1712 is the corresponding CA.<br><br>>Then, are you correctly applying "define = -DDDISRES" in your .mdp as I<br>>suggested previously?<br><br>I did correctly use the -DDDISRES, as suggested by you, which is as follows:<br><br>title = ${MOL}<br>cpp = /lib/cpp<br>define = -DDDISRES<br><br><br>Thanks & regards,<br>Latha.<br><br><br>----- Original Message -----<br>From: "Justin A. Lemkul" <jalemkul@vt.edu><br>Date: Wednesday, September 3, 2008 5:36 pm<br>Subject: Re: Bonds break while Minimising using distance restraints<br>To: plmallip@mail.uh.edu, Gromacs Users' List <gmx-users@gromacs.org><br><br>> <br>> <br>> plmallip@mail.uh.edu wrote:<br>> > Hi Justin,<br>> > <br>> > Thanks for your prompt <br>> suggestions. I hope I didn't cause any <br>> > sort of inconvenience by E-mailing you directly. <br>> > <br>> <br>> I say this constantly - it is always better to keep the <br>> discussion on the list <br>> so that, if I don't have the complete right answer (which <br>> happens often!) <br>> someone else can weigh in and help out. It is also helpful <br>> to complete <br>> discussions in the archives. There's nothing more <br>> frustrating than finding your <br>> exact problem in the archives, only to find out that the thread <br>> dies off without <br>> a solution :)<br>> <br>> > >I thought you were applying a 12-nm distance restrain <br>> to atoms in the <br>> > 7000's, so<br>> > >I'm confused as to why atoms615 1 and 6160 should be 12 <br>> nm apart <br>> > (assuming, of<br>> > >course, that you meant to say nm instead of A :)<br>> > <br>> > I am sorry for the confusion. <br>> The atoms are separated by 12 A (1.2 <br>> > nm). The atoms I restrained are 1703 & 1712 (6151 & 6160 atoms <br>> are also <br>> > from the same residues). These are the residues that looks as <br>> if they <br>> > are no bonds between them. ( residues alone, peptide bond <br>> alone and the <br>> > rest of the protein).<br>> <br>> How is it that atoms that are 900 indices apart are in the same <br>> residues. I <br>> don't understand. Do you mean that all four of these atoms <br>> are in the same <br>> residue? Then they definitely aren't amino acids! <br>> Are these two separate <br>> residues bridged by a distance restraint, that you are <br>> considering one residue? <br>> Is there some bond defined in the topology between *any* <br>> of these atoms?<br>> <br>> > <br>> > While doing grompp I get the following "removed 1 distance <br>> restraints". <br>> > Does this mean, the distance restraint isn't imposed at all?<br>> > <br>> <br>> That would be a pretty clear indication to me that distance <br>> restraints are not <br>> being applied.<br>> <br>> > I corrected the distance restraints I used as<br>> > <br>> > #ifdef DDISRES<br>> > [distance_restraints]<br>> > ;ai aj type index type' low up1 <br>> up2 fac<br>> > 1703 1712 1 0 <br>> 1 1.15 1.20 1.25 1.0<br>> > #endif<br>> > <br>> <br>> Then, are you correctly applying "define = -DDDISRES" in your <br>> .mdp as I <br>> suggested previously?<br>> <br>> http://www.gromacs.org/pipermail/gmx-users/2008-September/036136.html<br>> <br>> -Justin<br>> <br>> > I endup with the same error. Is there any possible way to get <br>> over this <br>> > problem?<br>> > <br>> > I appreciate your help in this regard.<br>> > <br>> > wamr regards,<br>> > Latha.<br>> > <br>> > <br>> > > There is no chance of <br>> steric clashes between 6151 & 6160. They are<br>> > > seperated by 12 A. ("Warning: 1-4 interaction between <br>> 6151 and 6160 at<br>> > > distance 1.387 which is larger than the 1-4 table size <br>> 1.000 nm. These<br>> > > are ignored for the rest of the simulation. This <br>> usually means your<br>> > > system is exploding") I cannot build the missing <br>> residues without<br>> > > knowing the secondary structure. I am already running <br>> one simulation<br>> > > with built residues. But, my ultimate goal is to run <br>> dynamics with<br>> > > distance restraints.<br>> > <br>> > Are you sure you are identifying the correct atoms? A 1-<br>> 4 interaction <br>> > involves<br>> > atoms that are very close together (in fact, three bonds <br>> away). Are you <br>> > saying<br>> > that they are separated by 12 A (1.2 nm) or by 12 nm? If <br>> they are <br>> > starting 12 A<br>> > (1.2 nm) away, then the error message still makes sense. <br>> If they are 12 nm<br>> > away, then I suspect that some sort of bond or restraint is <br>> being applied<br>> > improperly.<br>> > <br>> > <br>> > <br>> > I thought you were applying a 12-nm distance restrain to atoms <br>> in the <br>> > 7000's, so<br>> > I'm confused as to why atoms615 1 and 6160 should be 12 nm <br>> apart <br>> > (assuming, of<br>> > course, that you meant to say nm instead of A :)<br>> > <br>> > -Justin<br>> > <br>> > ><br>> > > My sytem is <br>> an pentamer. Here is the toplogy file<br>> > ><br>> > > ; Include forcefield parameters<br>> > > #include "ffG43a1.itp"<br>> > ><br>> > > ; Include chain topologies<br>> > > #include "chnrc_A.itp"<br>> > > #include "chnrc_B.itp"<br>> > > #include "chnrc_C.itp"<br>> > > #include "chnrc_D.itp"<br>> > > #include "chnrc_E.itp"<br>> > ><br>> > > ; Include water topology<br>> > > #include "spce.itp"<br>> > ><br>> > > #ifdef POSRES_WATER<br>> > > ; Position restraint for each water oxygen<br>> > > [ position_restraints ]<br>> > > ; i funct <br>> fcx fcy fcz<br>> > > 1 <br>> 1 1000 1000 1000<br>> > > #endif<br>> > ><br>> > > ; Include generic topology for ions<br>> > > #include "ions.itp"<br>> > ><br>> > > [ system ]<br>> > > ; Name<br>> > > Protein in water<br>> > ><br>> > > [ molecules ]<br>> > > ; Compound #mols<br>> > > <br>> Protein_A 1<br>> > > <br>> Protein_B 1<br>> > > <br>> Protein_C 1<br>> > > <br>> Protein_D 1<br>> > > <br>> Protein_E 1<br>> > > <br>> SOL 55419<br>> > > <br>> NA+ 54<br>> > ><br>> > ><br>> > > Thanks & regards,<br>> > > Latha.<br>> > ><br>> > > > > plmallip@mail.uh.edu wrote:<br>> > > > ><br>> > > > > Hi Justin, thanks for your response. You are <br>> right. I get the<br>> > > > following<br>> > > > > message in the .job file<br>> > > > ><br>> > > > > "Warning: 1-4 interaction between 6151 and <br>> 6160 at distance<br>> > > > 1.387 which<br>> > > > > is larger than the 1-4 table size 1.000 nm<br>> > > > > These are ignored for the rest of the simulation<br>> > > > > This usually means your system is exploding"<br>> > > > ><br>> > > > > The atoms I restrained are 1703 & 1712 (6151 <br>> & 6160 atoms are<br>> > > > also from<br>> > > > > the same residues). The distance between <br>> them is 12 A (there<br>> > > > are 14<br>> > > > > missing residues in between). My aim is to <br>> use distance<br>> > > > restraints,<br>> > > > > without building missing residues in <br>> between. Is there any way<br>> > > > I can<br>> > > > > overcome this warning why minimizing the system?<br>> > > ><br>> > > > It's very hard to say, because none of us <br>> knows what's in your<br>> > > > system, topology,<br>> > > > or how you built things :)<br>> > > ><br>> > > > You have some type of nasty steric clash <br>> that's driving atoms<br>> > > > 6151 and 6160<br>> > > > apart. Visualize the trajectory (.trr) <br>> to see if you can<br>> > > > identify where things<br>> > > > start to break down. I don't know if the <br>> distance> > > restraint has anything to do<br>> > > > with the problem or not.<br>> > > ><br>> > > > Is there a problem with building missing <br>> residues? That<br>> > > > might make life quite a<br>> > > > bit easier in the long run.<br>> > > ><br>> > > > -Justin<br>> > > ><br>> > > > ><br>> > > > > Thanks & regards,<br>> > > > > Latha.<br>> > > > ><br>> > > > ><br>> > > > > > Dear colleagues,<br>> > > > > ><br>> > > > > > I need to use simple distance <br>> restraints of 12.5 A<br>> > > > between two CA atoms<br>> > > > > > of two residues. I am using the <br>> following lines in the<br>> > > > .itp file<br>> > > > > ><br>> > > > > > #ifdef DDISRES<br>> > > > > > [distance_restraints]<br>> > > > > > ;ai aj type index type' low<br>> > > > up1 up2 fac<br>> > > > > > 1703 1712 1<br>> > > > 0 1 <br>> 11.5 12.0<br>> > > > 12.5 1.0<br>> > > > > ><br>> > > > > > The first feww line of .mdp file for <br>> minimisation of<br>> > > > protein alone is<br>> > > > > ><br>> > > > > > ; Preprocessing<br>> > > > > > ;<br>> > > > > ><br>> > > > <br>> title = ${MOL}<br>> > > > > ><br>> > > > <br>> cpp = /lib/cpp ;Preprocessor<br>> > > > > ><br>> > > > <br>> define = -DDISRES ;For cg, and also steep<br>> > > > > ><br>> > > > ><br>> > > > > You are not actually applying your distance <br>> restraint.> > > If you have "#ifdef<br>> > > > > DDISRES," then you would have to "define = -<br>> DDDISRES" in the<br>> > > > .mdp file.<br>> > > > > What<br>> > > > > you probably meant to define was "#ifdef <br>> DISRES" in the topology.<br>> > > > ><br>> > > > > ><br>> > > > After minimisation, the restarined residues & <br>> the adjacent<br>> > > > > > bonds break. This results in <br>> fragmnets - residues<br>> > > > alone, peptide bond<br>> > > > > > alone and the rest of the protein. <br>> The distance<br>> > > > restrained residues<br>> > > > > > seems to try to move towards each <br>> other (6.04 A after<br>> > > > minimisation) and<br>> > > > > > this might have caused <br>> fragmentation. I tried to use<br>> > > > various upper and<br>> > > > > > lower values for bond length so as <br>> to increase<br>> > > > flexibility. But, still I<br>> > > > > > end up in the fragments.<br>> > > > > ><br>> > > > ><br>> > > > > Bonds don't break in classical MD, this is <br>> just an artifact of<br>> > > > > visualization,<br>> > > > > probably from nasty steric clashes within <br>> your structure.<br>> > > > ><br>> > > > ><br>> > > > > <br>> > Some<br>> > > > of the suggestions in the archive says VMD <br>> doesn't show<br>> > > > > > bonds if they r above threshold <br>> value. When I checked<br>> > > > the distances<br>> > > > > > between the atoms, one of them is <br>> really long CO-CA<br>> > > > bond 3.23 A<br>> > > > > > (normally its 1.59A). This means the <br>> bond is no longer<br>> > > > there.> ><br>> > > > ><br>> > > > > No, the bond is there, VMD just isn't smart <br>> enough to see it<br>> > > > :) You are<br>> > > > > probably well on your way to an explosion if <br>> you try to<br>> > > > constrain bond<br>> > > > > lengths<br>> > > > > with LINCS, however.<br>> > > > ><br>> > > > > -Justin<br>> <br>> -- <br>> ========================================<br>> <br>> Justin A. Lemkul<br>> Graduate Research Assistant<br>> Department of Biochemistry<br>> Virginia Tech<br>> Blacksburg, VA<br>> jalemkul[at]vt.edu | (540) 231-9080<br>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<br>> <br>> ========================================<br>>