Re: [gmx-users] specbond recognised but not built

Hi Grange, It recognizes the possibility of having a bond between these atoms. That's where the distance matrix comes in. But if a bond were made, you'd have a statement right after the distance matrix saying something like "linking atom ... and atom ...". It doesn't happen, and the reason is the

Re: Re[2]: [gmx-users] RE: can gmx be used to simulation NaCl

As I stated in the first sentence, I doubt the usefulness of classical MD for simulating crystallization of NaCl. Whatever I state after that applies to the case of trying it with classical MD nonetheless. Please read closely before trying to outwit however you find on this list. Second, as is cle

Re: [gmx-users] High number of steps are adding

Hi Sudheer, I would say you just try to add a nanosecond to a run which still has ten to go (10+1=11). That also tells me you're not trying to extend a run already performed (properly), as it has a starting step of 0 (starting time 0.000). Then on another note, it seems that you didn't copy-paste

Re: [gmx-users] Magic number error

Hi Minnale, You could try another version as was suggested... Never hurts to try. The magic number error occurs if the file is screwed. trjconv will correctly process the trajectory up to the point where the magic number error occurs, so you can restart from the last good entry in the file. Out of

Re: [gmx-users] Protein is moving out of box.

Hi, Well, I think it should also be incorporated into (Gromacs) MD tutorial material. It's on my to do list. I don't think there's much use in adding a message in the mdrun output (might as well always add it, not even checking for jumps). It's basic PBC, which, with a bit of thinking, can be unde

Re: [gmx-users] RE: can gmx be used to simulation NaCl

Hi William, I'm not very sure you can simulate crystallization of salt with classical MD. In any case, the force field is not parameterized to reproduce crystallization or melting c.q. the melted state of NaCl. It's therefore unlikely that it will produce meaningful results. The best approach :) w

Re: [gmx-users] RE: Protein is moving out of box.

Hi, That doesn't necessarily "fix" the "problem". Which position of the protein is taken as a reference depends on the position of the first atom. Gromacs wants to have the first atom of a molecule in the rectangular unit cell at the origin. Even if you set comm removal for the group, the initial

Re: [gmx-users] Protein is moving out of box.

Browse the archives, check the wiki. http://wiki.gromacs.org/index.php/Periodic_Boundary_Conditions Tsjerk On Fri, Jun 27, 2008 at 8:06 AM, Bhanu <[EMAIL PROTECTED]> wrote: > Hi all, > am new to Gromacs. I tried a 10 ps simulation with a protein and after the > run, the protein came out of the bo

Re: [gmx-users] disulphide bonds

Hi, The only thing I can think of is that you've run pdb2gmx already and added the termini (adding H1 H2 and H3 for the terminus, which causes the complaints). Now, you're running pdb2gmx for the second time (right?) to merge the chains. Next to -ignh you can also try to simply remove these N-term

Re: Re: [gmx-users] Understanding about the deleted trajectory file

Minnale, A file is (generally) data on a disk, of which the operating system knows where it is. Knowing where the file is depends on the inode of the file. Deleting a file is usually removing the inode, not the data. But once the inode is removed, the data can no longer be recognized as a certain

Re: [gmx-users] disulphide bonds

Hi Ram, Check the option -merge of pdb2gmx. Cheers, Tsjerk On Thu, Jun 26, 2008 at 6:11 AM, rams rams <[EMAIL PROTECTED]> wrote: > Dear Gromacs users, > > Is there any way to handle the disulphide bond formed between two > independent fragments of a protein ? Precisely it is an inter disulphide

Re: [gmx-users] PCA uses average structure or reference structure

Hi Sunita, You should check the manual on this (and some statistics texts on PCA). g_covar calculates the average structure and takes the deviations around this average for further calculations. In that respect, you should be save. But the fact that you pose this question indicates that you may be

Re: [gmx-users] Retrieving .trr file?

Hi Minnale, You could've checked the archives. Searching on "trr" and "deleted" would have yielded (among others): http://www.gromacs.org/pipermail/gmx-users/2008-May/034217.html Tsjerk On Tue, Jun 24, 2008 at 5:40 AM, minnale <[EMAIL PROTECTED]> wrote: > > Hi gmx users, > I have deleted

Re: [gmx-users] Newbie question

Hi, Of course I can't add anything to the comments regarding the solvent and ions ;) The #include "ions.itp" is commonly added through pdb2gmx in the >3.1 versions, so it shouldn't be necessary to add that (and it isn't for the tutorial (v3.3.3). Anyway, it's good to keep in mind though that the i

Re: [gmx-users] RE: mdp files

Hi, For a tutorial and a workflow you can also check out: http://www.nmr.chem.uu.nl/~tsjerk/course/md-tutorial/ http://www.nmr.chem.uu.nl/~tsjerk/course/md-tutorial/01-Preparation-Workflow.jpg A bit in progress still, and any comments welcome ;) Cheers, Tsjerk On Sat, Jun 21, 2008 at 9:40 AM,

Re: [gmx-users] RE: modelling a new molecule in OPLS

Anandita, Just to add my response on the pile (and do take the previous advice) what you show here displays a problem of yours with respect to molecular dynamics simulations. That naming should be consistent, sure, if you know what you're doing you can sort of ignore warnings like 'atom names don'

Re: [gmx-users] problem with new sugar residue

Hi Carmen, Well, adding a residue to aminoacids.dat only makes sense for amino acids (although I admit to fiddle it sometimes, in which case it is usually best to make a local copy). But one thing with amino acids is that backbone -N(H)-Ca-C(O)- thing, which is referred to in the termini database.

Re: [gmx-users] genion

Hi sh-karbalaee, Well, running an MD simulation has nothing to do with genion per se. But it's better not to have a net chare in your system. Therefore you'd best add an ion (at the least) to your system with unit charge. Whether you do that using genion or do it by hand, is entirely up to you. Ch

Re: [gmx-users] problem with new sugar residue

Hi Carmen, You really have to be careful to match the .rtp to the .pdb building block. pdb2gmx indicates that there's an atom in the .pdb file, which is not found in the [ CHIT ] entry in the .rtp file. If you want better help, you'll have to ask a better question: you should provide more details

Re: [gmx-users] basic units: acceleration conflict (revision)

Hi Nadir, First of all, nm / ps^2 for acceleration was not a choice, but a consequence of other choices. Second, it's meaningless to pull this out of context. There's no reason whatsoever not to have a huge accelaration, if it is only for short times. It's the speed that counts, not the accelerati

Re: [gmx-users] Define: Energy groups

Hi Tuhin, It depends on what you do. In both cases you will have to run grompp with an index file with a group specified, containing both the Protein and the calcium ion. You can take an existing index file (created simply with "echo q | make_ndx -f mystructure.gro") and add the number of the calc

Re: [gmx-users] Re: pbc-replica exchange-trjconv

Hoi Servaas, Was that the trajectory for a given temperature, or for a given system? It should be for the latter, as otherwise, there will be weird shifts introduced. A trajectory for a given system, over the different conditions should be (from the PBC point of view) continuous and it should be p

Re: 回复： Re: 回复： Re: [gmx-users] 2D pro jection and corresponding conformation

Xi Zhao, If you know these steps are normal, how come you don't know how to go about? A projection on the plane spanned by two eigenvectors is the projection of your structure onto one of these eigenvectors plotted against the projection of your structure on the other. Each structure, and therefor

Re: [gmx-users] pbc-replica exchange-trjconv

Hi Servaas, > trjconv -f fit.trr -o cluster.trr -n lig_prot.ndx -pbc cluster -s top140.tpr I think there's quite a bit of reason to start calling you names here :) Assumedly, fit.trr means that it results from fitting the trajectory to a reference? So what does this do with your PBC? > I also tr

Re: [gmx-users] calculating ionic strength

Hmmm, Now imagine your simulation system as a say 1000 nm3 portion of a liter. For that liter you work out the number of ions and you properly translate that into an amount of ions you expect in the 1000 nm3. But then your protein (floating along in the same liter in some small concentration) cros

Re: [gmx-users] Melting temperature of the potato, a bug in grompp?

Hi Xavier, Have you checked the genome and made sure your potato did not suffer from any infection? This will have a significant effect on the melting temperature. Maybe it helps if you link an image of the potato at the end of the simulation. Tsjerk On Sun, May 11, 2008 at 12:23 AM, Xavier Peri

Re: [gmx-users] Re: g_rms: Too many iterations in routine JACOBI

Hi, Maybe good courtesy to sign with a bit more than some initials. It's so much nicer to have a bit of the impression to know whom you're talking to. As for the question, if you would select 'Protein' to extract a part of your system to a trajectory, this part would likely be the first N atoms f

Re: [gmx-users] g_rms: Too many iterations in routine JACOBI

Hi JS RED, This usually indicates that you have a mismatch between your reference structure and your trajectory, which is logical as you extracted a specific set of coordinates from the trajectory, but used an original (complete) gro file. Hope it helps, Tsjerk On Thu, May 8, 2008 at 9:18 AM, m

Re: [gmx-users] box vectors entry in "gro" file

Hi David/Makoto, I wouldn't call it a stupid error, keeping nine numbers for the definition of a box. Of course in simulation the lower triangular part of the box matrix is zero. But if you reorient the system and want to preserve PBC (like after fitting), the box will be rotated and the full matr

Re: [gmx-users] (no subject)

Hi Arnab, If you know the time at which you want to start the analysis, you can use the -b option (with whatever analysis tool). E.g. starting rmsf calculation at 1 ns: g_rmsf -s topol.tpr -f traj.xtc -o rmsf.xvg -b 1000 Cheers, Tsjerk On 5/5/08, Arnab Senapati <[EMAIL PROTECTED]> wrote: > Hi,

Re: [gmx-users] rtp files

I beg your pardon. What do you think we are? The equivalent of a fast-food take-away? Or a service for doing your homework for you? Do take a good read of http://catb.org/~esr/faqs/smart-questions.html Tsjerk On Mon, Apr 21, 2008 at 1:28 PM, shahrbanoo karbalaee <[EMAIL PROTECTED]> wrote: > hi a

Re: [gmx-users] Bad .tpr or .xtc files?

matching reference structure? > > Thanks a lot! > > Peggy > > > > On Thu, Apr 10, 2008 at 11:52 AM, Tsjerk Wassenaar <[EMAIL PROTECTED]> > wrote: > > Hi Peggy, > > > > The key thing is that there's a mismatch between your .tpr file and > &

Re: [gmx-users] Bad .tpr or .xtc files?

, I had: xtc_grps = protein Ca Cl > > Will this difference cause the problem? How should I solve it? Thanks a lot! > > Peggy > > > > On Thu, Apr 10, 2008 at 12:22 AM, Tsjerk Wassenaar <[EMAIL PROTECTED]> > wrote: > > > Hi Peggy, > > > > I suspect that

Re: [gmx-users] Bad .tpr or .xtc files?

Hi Peggy, I suspect that in your .mdp file you have a line xtc-grps = Protein This means that the xtc file will only contain those atoms which gromacs reckognizes as amino acids, based on the list in the file aminoacids.dat. Your .tpr file which is used to base the index on, contains all atoms,

Re: [gmx-users] recognising phos group

Hi Jayant, PO3 seems to me the anion of metaphosphoric acid, not much to do with phosphoric acid. The latter could be sort of extracted from phosphoric acid containing residues, although that doesn't give guarantees for good behaviour. Also, I wouldn't count on the PO4 parameters thus extracted to

Re: [gmx-users] recognising phos group

here. Sorry for the previous babbling... The reference to the wiki still goes though Cheers, Tsjerk On Wed, Apr 9, 2008 at 9:24 AM, Tsjerk Wassenaar <[EMAIL PROTECTED]> wrote: > Hi Jayant, > > PO3 seems to me the anion of metaphosphoric acid, not much to do with > phosph

Re: [gmx-users] g_sas WARNING: could not find a Van der Waals radius

Hi Jo, > > Also if I am comparing the SASA for the enzyme in > > three different simulations were only the ligand (for which all radii are > > defined) differs, would this have a huge effect on the results? Your question is semantically garbled. You comparing anything should not influence the

Re: [gmx-users] Command for MD

Dear Lal, It would help if you mentioned the commadns you used and whatever else you tried. Maybe it's a good time to read http://catb.org/~esr/faqs/smart-questions.html Tsjerk On Sat, Mar 29, 2008 at 8:56 AM, s lal badshah <[EMAIL PROTECTED]> wrote: > Dear Experts, > Hi, I have done equilibrati

Re: [gmx-users] ED analysis, domain rotation, DynDom

ot quite sure > about the reference to the pair of pdb files. Would a way to do this be to > say project the first and second eigenvector and then use Dyndom to compare > the starting structure with the first eigenvector extreme pdb and then do > the same for the second? Would this sh

Re: [gmx-users] pdb2gmx error

No, but you should try to distinguish an O (letter-O) from a 0 (numeric zero). Tsjerk On Wed, Mar 19, 2008 at 3:54 PM, Gadzikano Munyuki <[EMAIL PROTECTED]> wrote: > I want to do dynamics on a cyclic polypeptide. The peptide contains a residue > that is not standard Ornithine. I have added [ORN]

Re: [gmx-users] center of mass removal

as not able to download the modified versions of the code at > http://md.chem.rug.nl/~tsjerk/GMX/ where this method is implemented. > I was wondering if anyone has implemented it in some newer version of > gromacs as Tsjerk Wassenaar did for 3.2.1. > > I am reading the relevant pape

Re: [gmx-users] How to create three different zones to minimize energy of a enzyme?

Hi Lacerda, You should be cautious in the interpretation of your results. Your active site will only be minimized in potential energy in the context of your frozen surface and your restraint internal degrees of freedom. You should be very confident that your surface is about correct and your inter

Re: [gmx-users] equilibration

Hi Lal, Well, if you set the number of steps to 0, it should get you rid of any errors. But for the rest, the LINCS errors don't have to do with the length of the simulation but with what's in there.You can try and decrease the time step as is suggested by the program. But the LINCS error is likel

Re: [gmx-users] Whereabouts of NDLP???

Hi Alan, Unfortunately there have been server problems (severe hacking) in Groningen some while ago, and the NDLP server was terminated. But, we're right about to reestablish an improved server here in Utrecht. This server will be much faster, seconds rather than hours - the optimal packing for th

Re: [gmx-users] ED analysis, domain rotation, DynDom

Hi Jo, First of all, you should note the difference between essential dynamics analysis and sampling. Also note there's nothing essential about it. But the first is done using g_covar/g_anaeig and the latter, which concerns enhanced sampling along specific modes, is done using make_edi/mdrun. So i

Re: [gmx-users] Data generated by g_sas

Monika, Daniel has already given the answer. The third column gives the standard deviation, whereas the second gives the average SAS. You could've found this answer also by browsing the mailing list archive, as this is one of those questions being posted every once in a while... Cheers, Tsjerk

Re: [gmx-users] creating trajectory with ligand close to the protein

Hi David, If you use a structure file (.gro/.pdb) which corresponds to the starting structure and has the protein and ligand in the right place, you can do it with trjconv -pbc nojump. Cheers, Tsjerk On Sun, Feb 24, 2008 at 4:47 AM, David Osguthorpe <[EMAIL PROTECTED]> wrote: > On Sun, Feb 24,

Re: [gmx-users] Temparature and density

Hi Chandu > Because I am using NPT ensemble will it automatically adjust to that > density? (because box size will increase under high temperature and > constant pressure therefore density will be decreased) Yes. But don't expect to get right on with the density (or viscosity/diffusion/...).

Re: [gmx-users]build topology file for a molecule define with new residues

Hi Justin (and Geraldine), I think that cross-referring people asking about building topologies to the exotic species wiki page by default is a bit too much. It's Parameterization they need to read (and chapter 5 of the manual). Exotic species are those weird atoms you sometimes encounter in ligan

Re: [gmx-users] Dose the GROMOS FF favour beta-sheets?

Hi Pascal, Please specify the (Gromos) force field used further. There seems to be something with the 53a5/6 series in terms of alpha helix / beta sheet preference. I'm not sure whether this has been fixed already. I don't recall having heard of such an issue with the 43a2/45a3 series. But these h

Re: [gmx-users] How to ask pdb2gmx to print all parameters in the itp file

Hi, grompp allows you to write the (cpp) processed topology (-pp). Since many parameters are controlled using cpp #define statements, cpp has to be called to fill the values. pdb2gmx can't do that. Cheers, Tsjerk On Feb 15, 2008 6:46 PM, Alan Dodd <[EMAIL PROTECTED]> wrote: > If you convert the

Re: [gmx-users] abnormal RMSD

Hi, You may have written only a subset of atoms to the new trajectory files using trjconv. Keep track of what you're doing and what is in which file. Besides, most analysis tools also accept .pdb/.gro files for reference. Cheers, Tsjerk On Feb 15, 2008 6:31 PM, Justin A. Lemkul <[EMAIL PROTECTE

Re: [gmx-users] eigenvalues as a function of time

ord, after all. Even > now I can't find the right word. I slipped up twice. > > I apologize for my mistake -I basically took from you a few minutes > because of my lack of clarity :) > > Cheers, > Michel > > > > On Thu, Feb 14, 2008 at 11:47 PM, Tsjerk

Re: [gmx-users] eigenvalues as a function of time

Hi Michel, You're principal components will be heavily undersampled (and therefore underdetermined), most notably the higher ones. You're likely not even to have more than a single uncorrelated observation per subtrajectory. The eigenvalue is a measure of the fluctuation, or actually the spread, o

Re: [gmx-users] Hello

Hi Anamika, It would be good to do some background reading on MD. For this issue, you most likely should read: http://wiki.gromacs.org/index.php/Periodic_Boundary_Conditions Cheers, Tsjerk On Feb 12, 2008 11:14 AM, Anamika Awasthi <[EMAIL PROTECTED]> wrote: > Dear Gromacs users, > I am b

Re: [gmx-users] Proline on OPLSSaa

Hi Mauro, The .top says it all: you haven't specified parameters. Just listing the bonds, angles and dihedrals in the .rtp file is not enough. You'll have to assign parameters to them. Check the entries (notably PRO and ACE) in the .rtp file of your choice... Cheers, Tsjerk On Feb 11, 2008 12:0

Re: [gmx-users] (no subject)

Please do give your post a descriptive title... You likely have a serious problem with your topology or with your simulation cell. Can't tell without more information. Did grompp give any warnings? Double check your input. Cheers, Tsjerk On Feb 7, 2008 9:44 AM, mahendra awale <[EMAIL PROTECTED]

Re: [gmx-users] Gro file with more than 99999 atoms

Hi Adama, Internally, the atom number is neglected. You can have them all at 1 ;) The residue numbers are sort of neglected, but a change in residue number is recorded as a change in residue. The most important thing is the number on the second line... (and the topology if you want to start a simu

Re: [gmx-users] Change in .gro in grompp

Hi Caleb, You can use editconf to extract the coordinates from your .tpr file (but these will be the same as those in the input file used). My guess (and Mark's) is that you placed a slab on either extreme of your unitcell, which makes them occupy the same space in the infinite simulation system.

Re: [gmx-users]query regarding unfolding of protein at higher temperature

Hi Sangeeta, > > 1) Will the result be erroneous if I keep box size unaltered at higher > temperature? If your protein starts unfolding, you are likely to get direct interactions between your periodic images. That will severely distort your results (to the point that you can not draw conclus

Re: [gmx-users] Turn off the diheral energy

Hi Myunggi Yi, > > Mixing force fields is an intrinsically bad idea. See > http://wiki.gromacs.org/index.php/Parameterization > I second that... > > Is it possible to turn off dihedral energy (proper and improper) for a > > certain molecule? > > If yes, then how can I do this? > > Comment out th

Re: [gmx-users] Which forcefield should I use?

Rui Li, That's part of your homework. Checking the literature on similar systems and do background reading on MD and force fields. Also read http://catb.org/~esr/faqs/smart-questions.html or http://www.lat30n.cn/doc/oss/smart-questions.html and http://wiki.gromacs.org/index.php/Parameterizatio

Re: [gmx-users] image control

x27;m attaching the file to you (Tsjerk Wassenaar). > Again I didn't do any modification. This is a just output from MD. > As you know you can check the coordinate in the .gro text file. > This is not a visulalization problem. > If any body wants, I will send you my .gro file. &

Re: [gmx-users] image control

Hi Myunggi Yi, In addition, it may help if you give some examples: link the structure file, the topology file, and some sample images highlighting the point your trying to make. Apparently, leaving us guessing doesn't help. Tsjerk On Jan 16, 2008 12:10 AM, Mark Abraham <[EMAIL PROTECTED]> wrote:

Re: [gmx-users] image control

Hi Myunggi Yi, Did you by chance use trjconv prior to visualization? If so, what options did you use? mdrun doesn't write broken molecules. Cheers, Tsjerk On Jan 15, 2008 8:48 PM, Justin A. Lemkul <[EMAIL PROTECTED]> wrote: > Quoting Myunggi Yi <[EMAIL PROTECTED]>: > > > I don't think this is

[gmx-users] Fwd: x2top

Kinshuk, > Hi , > I have gone through gromacs mailing list there i came to know that u > have faced same problem while executing the command x2top. Performing a search on my name and x2top, I find three entries, none of which give just a hint of me having used x2top, nor of me having had problems

Re: [gmx-users] Generating topology file for a molecule (FNP) not in the gromacs library.

Hi, Contrary to Chris, I think it's easier/better to leave the .rtp database for building blocks of chains (and definitely advocate against bothering with the file for newbies). Small ligand topologies are better made seperately "by hand" and inserted in manner similar to the procedure in John Ker

Re: [gmx-users] Re: gmx-users Digest, Vol 45, Issue 30

Hi Prasad, You also have to reckon that the RMSD is always positive, so the average RMSD will also always be positive. It's a chi-variate. Try some thought experiments with distances, average distances and distances to an average position. Cheers, Tsjerk On Jan 10, 2008 8:09 PM, David van der S

Re: [gmx-users] use do_dssp with only pdb file with many configurations in it

Hi Stefane, On Jan 10, 2008 3:03 PM, ABEL Stephane 175950 <[EMAIL PROTECTED]> wrote: > Hi gromacs users > > In previous message Mark Abraham. said me that do_dssp tools can be used > only with a pdb file (thank to him ;))). I am newbie with gromacs (i came > from the ORAC MD world), so i have two

Re: [gmx-users] How can I add ffG43a1p force field to gromacs software?

Hi Mitra, You can add it in the file FF.dat in the $GMXDIR/share/gromacs/top/ directory. Cheers, Tsjerk On Jan 8, 2008 3:35 PM, Mitra Kheirabadi <[EMAIL PROTECTED]> wrote: > Dear Dr. Smith > > I want to run a virus phosphorylated protein by gromacs. Furtunatly, you > construct related force fi

Re: [gmx-users] Drug-Enzyme Tutorial

Hi Swapna, The PRODRG server generates topologies for the gmx force field (ffgmx; deprecated!). You most likely want to have a topology compliant with the Gromos96 force fields (e.g. ffG43a2). For this you need to use the beta version of the PRODRG server. Mind you that force field parameterizati

Re: [gmx-users] Gromacs version

Hi Raghu, Try any of the pograms (with the -h flag) and the header will tell you which version you have... Cheers, Tsjerk On Jan 5, 2008 8:38 AM, Ragothaman Yennamalli <[EMAIL PROTECTED]> wrote: > Hi, > Can anyone please tell me how to find which version of > gromacs is installed in a particul

Re: [gmx-users] g_rmsf fitting

ein in ref1.tpr and part of subunits are out of box. > I do not know if this can be called jump. > > Tang > > > Tsjerk Wassenaar wrote: > > Hi Tang, > > > > The subunits have no contact each other obviously, > > without jump in them and I can not see an

Re: [gmx-users] g_rmsf fitting

Hi Tang, The subunits have no contact each other obviously, > without jump in them and I can not see an intact protein. Please be more clear and try to write full, correct sentences. I suppose you mean that the subunits are separated at start, so there has been a jump in the setup stage. Howeve

Re: [gmx-users] g_rmsf fitting

Hi Tang, It's just the general case of least-squares fitting: 1. Bring centres of geometry/mass to origin 2. Calculate (mass-weighted) rotation matrix 3. Rotate structure (4. Calculate squared displacements) But what do you mean with 'very different'. Can you provide an example? What command lin

Re: [gmx-users] RMSD calculations by g_rms

Hi Monika, Xavier, You can't really judge a run from the rmsd ;) g_rms and VMD should the exact same result. You might check the reference > frame you use and make sure you fit your protein using the same set of > atoms. > I concur, and Xavier, you hit the spot with referring to the reference fr

[gmx-users] Fwd: Residue 'COA' not found in residue topology

Hinge, Please keep discussions on the list, there may be others which have the same question. Also try to put some effort in writing a well readable e-mail. User list conversations are not school notes. In answer to your question... I'd start with a literature search. Plenty of people will have p

Re: [gmx-users] Residue 'COA' not found in residue topology database

Hi Hinge, pdb2gmx is intended to convert protein/nucleic acid chains into topologies. It's not a magical program to convert whatever compound into a topology. Just what it says, there's no residue COA in the database for the force field you're trying to use. Check another force field or try to fin

Re: [gmx-users] center of mass removal

Hi, Just to add my 5 cEUR. The flying ice cube will be avoided using linear comm removal on the whole system (default), which will retain diffusion of the peptide in the solvent. The peaks you see in the comm I guess are due to the update of the neighbour list (every ten steps?). This will change

Re: [gmx-users] Re: Density Deferences between spc216 and tip4p

Chandu, It's clear you didn't do the calculations. Please do them yourself and see what answer you get for the density of 32885 water molecules in a box with volume 10^3 nm^3. Note also that there may be implicit assumptions underlying the value of the density provided by genbox, but it's the numb

Re: [gmx-users] asking for recommendations

Hi Michelle, What reasons do you have suggesting factors other than modelling limitations? Is there experimental data regarding the time scale of uncoiling? I would guess it would take longer than 20 ns. Also, you should consider that you're looking at a single molecule. The observation of uncoili

Re: [gmx-users] pbc and tpr file

Hi Tang, It doesn't hurt to check (i.e. you should check ;)) whether the .tpr file contains the protein "in one piece", if you want to use it as a reference structure for rmsd calculations. You can extract the coordinates from the .tpr file using editconf and then have a look. Actually, you should

Re: Re: RE: Re: Re: [gmx-users] Energy minimisation

Hi Jestin, As I said, the last line in the .gro file codes for the box. So, you have a singular box! You probably did something wrong with editconf. Did you give it box dimensions at all (-box/-d). Have a look at the help: editconf -h Besides that, do have a look at the procedure you used to obta

Re: Re: [gmx-users] Energy minimisation

Jestin, Please don't use all capitals. As Mark has pointed out several times, that's considered shouting. You're probably frustrated that things don't work according to your expectations, but the frustration comes from you not knowing what your doing. Don't blame us for that, go read a manual. If

Re: [gmx-users] Problem with S-S bond

Hi Blaise, Disulfide bonds are only made when two Cys-S atoms are within 0.2 +/- 0.02nm from each other. This distance is in the file specbond.dat. You can search the archives for how to make the bond. Also, please start a new thread rather than replying to a message. Now there's debris unrelated

Re: [gmx-users] pdb2gmx error

Hi Tawhid, The file you got was in the format used by the _program_ GROMOS. But this format is not supported by pdb2gmx/Gromacs. The GROMOS _forcefield_ is a set of equations and parameters, which stands apart from the formatting of the building blocks. You could've at least taken a bit of effort

Re: [gmx-users] regarding .gro file

Hi, Maybe it's good to note that gromacs (mdrun) will always write the coordinates such that the first atom of each molecule is located inside the rectangular box spanned by the xx, yy and zz components of the triclinic box, located at the origin. Tsjerk On Nov 25, 2007 4:47 AM, Mark Abraham <[E

Re: [gmx-users] grompp

Hi Jestin, Read chapter 5 thoroughly :) It seems that in your topology file (minding the #includes) the directive [ system ] is given too early, e.g. before the definition of the [ moleculetypes ]. Tsjerk On 25 Nov 2007 05:51:50 -, JMandumpal <[EMAIL PROTECTED]> wrote: > Dear Gromacs users,

Re: [gmx-users] restart an amber run in gromacs

Hi Servaas, In addition to the other remarks, also consider what happens to your system when you instantly go from discarding all interactions beyond 8 angstrom to including all interactions in the periodic system (with PME). Tsjerk -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecu

Re: [gmx-users] how to get basic trajectory information out trjcat

Hi Maria, try gmxcheck Tsjerk On Nov 21, 2007 10:25 AM, maria goranovic <[EMAIL PROTECTED]> wrote: > Hi, > > Is there a utility which can output basic trajectory information like: > > - number of frames > - frequency of frame writing > > I tried using trjcat on my trajectory which is 27 frames,

Re: [gmx-users] Help with energy minimizing protein in water box with CA2+

Peggy, You really have to do some background reading on molecular dynamics simulations... After I ran an energy minimization, the CA2+ ended up outside of the box. > Now I am really perplexed. What could be causing this behavior? > See http://wiki.gromacs.org/index.php/Periodic_Boundary_Condit

Re: [gmx-users] Why so many energy minimization and position restrained simulation steps?

Hi Peggy, To understand the differencxes between the runs, you'll have to read and compare the .mdp files well. I'd suggest to start with the Gromacs manual, chapter 7. For one, position restraint MD depends on the presence of [ position_restraints ] in the topology and has nothing to do with the

Re: [gmx-users] *.gro output file being written to inverse

Hi Luciano, Did you use -shuffle/-sort with grompp? This can change the order of molecules. It will be changed in the .tpr and hence in all the structure output of mdrun (xtc/trr/gro). Cheers, Tsjerk On 11/1/07, Luciano Costa <[EMAIL PROTECTED]> wrote: > > Hi gmx'users, > > I runnning MD simula

Re: [gmx-users] Regarding Box-X Box-Y values from g_energy

Hi Sona, If you use isotropic pressure coupling, there will be a single scaling factor for all three dimensions. So if the box lengths are equal at the start, they will always remain equal. Best, Tsjerk On 11/1/07, Sona Aramyan <[EMAIL PROTECTED]> wrote: > > Thank you very much for your suggest

Re: [gmx-users] is there any size limit for simulation in gromacs

Hi Anupam, The problem will more likely be in the computational resources you have :) Definitely not in Gromacs... (as far as it concerns the feasibility of simulating a large protein in a membrane). Cheers, Tsjerk On 10/15/07, Anupam Nath Jha <[EMAIL PROTECTED]> wrote: > > > > Dear all > > i

Re: [gmx-users] Fatal error: Atom CA not found in residue LYSH200 while adding hydrogens

> > Tsjerk, > > I just started to learn Gromacs. But how do I check the missing atoms? > > Thanks, > > Haining > > On Wed, 10 Oct 2007 06:41:31 +0200 "Tsjerk Wassenaar" wrote: > > Haining, > > > > Did you check the structure for missing

Re: [gmx-users] Fatal error: Atom CA not found in residue LYSH200 while adding hydrogens

Haining, Did you check the structure for missing atoms/residues (REMARK 465/470)? Tsjerk On 10/10/07, Haining Liu <[EMAIL PROTECTED]> wrote: > > Hi, > > I have a problem using Gromacs. When I use the pdb2gmx command to > generate the .top and .gro files, I got the error: > >

Re: [gmx-users] restart md from the point it had stopped

;force to the .trr file, I think you > can't get a good continuation without that information. > > > On 10/8/07, Tsjerk Wassenaar <[EMAIL PROTECTED]> wrote: > > Hi Sarbani, > > > > Use tpbconv. You can only (properly) restart from a point where you have > a >

Re: [gmx-users] restart md from the point it had stopped

Hi Sarbani, Use tpbconv. You can only (properly) restart from a point where you have a frame with velocities (in the .trr file) and preferrably energies (.edr). Best, Tsjerk On 8 Oct 2007 12:34:23 -, sarbani chattopadhyay < [EMAIL PROTECTED]> wrote: > > > hi, > I have been running a molec

Re: [gmx-users] gmx continuation run

Hi Vijaya, Did you note that tpbconv -extend extends the _remaining_ runtime with the amount given. So if the frame used for the continuation run had 140 ps remaining and you use -extend 5, you'll have 145 to go. Tsjerk On 10/8/07, Mark Abraham <[EMAIL PROTECTED]> wrote: > > vijaya subramanian w

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