Re: [PyMOL] Pymol cavity detection error?

Hi Kanika, Try set two_sided_lighting Cheers, Tsjerk On Jun 28, 2017 17:14, "kanika sharma" wrote: > Dear PyMolers > > I want to see the cavities in my protein using the following steps: > > Setting → Surface → Cavities & Pockets Only. > Show surface > Cavity Detection

Re: [PyMOL] Problem with 'byring' selection

Hi Vijay, It is logic. 'byring elem N' selects all nitrogens and then expands the selection to include the rings in which these participate. 'elem N and byring elem N' does the same, but then intersects (and) to extract only nitrogens. But that is the same as 'elem N'. If you want to have the

Re: [PyMOL] Is it possible in Pymol to determine Individual Bond, Dissociation Energy for any Bond in organic molecules?

Dear Rajib, Pymol reads atom labels and positions from a coordinate file. It then determines which atoms are bonded based on distance criteria. That is used to draw the molecule. Pymol also has an internal library of molecules and fragments, with atoms and bonds, which can be used to build bigger

Re: [PyMOL] Is it possible in Pymol to determine Individual Bond, Dissociation Energy for any Bond in organic molecules?

Hi Rajib, The bonds are determined based on a distance cutoff. Hope it helps, Tsjerk On Jun 1, 2017 21:15, "Susmita/Rajib" wrote: How come we see structures of molecules in PyMol? https://en.wikipedia.org/wiki/PyMOL

Re: [PyMOL] Pymol fab ss = 4 introduces bends in the structure

Hi Ahmad, Because the chain contains prolines. These typically cause kinks in a chain. Cheers, Tsjerk On Fri, Apr 7, 2017 at 2:26 PM, Ahmad Abdelzaher wrote: > Hello, > > I used cmd.fab('sequence', ss=4) to create 1baz_linear_protein.pdb, > where sequence is the

Re: [PyMOL] Calculating center of mass for the entire protein

Hi Ahmad, The center of mass of an atom is its position. A function like cmd.centerofmass in the context of pymol only makes sense with a selection. E.g.: x,y,z = cmd.centerofmass('byres n. ca') print "COM of protein:", x, y, z Hope it helps, Tsjerk On Thu, Apr 6, 2017 at 6:30 AM, Ahmad

Re: [PyMOL] Scripting coloring method via own calculations

Hey :) Just as sidenote, the spectrum command takes arbitrary color schemes. Just combine colors separated by underscores. Also fun in combination with set_color :) Cheers, Tsjerk On Feb 14, 2017 5:46 PM, "Robert Campbell" wrote: Hello Peleg, I think there are

Re: [PyMOL] Pseudoatom for a cavity

Hi Kanika, That's been quite a while! Nice to see you again and to see you're still your determined self, still a bit impatient, reposting a message within a day :) The issue with the second question is not about center_of_mass, but about center_of_no_mass, which is a bit harder (and I don't

Re: [PyMOL] making a plane

Hi Vitaly, You have several options, but if the loops are nicely bent, the best is probably doing PCA on the coordinate sets of the loops and calculate the angle between the smallest eigenvectors. Is that enough information? Do you insist on drawing the planes? Cheers, Tsjerk On Jan 17, 2017

Re: [PyMOL] default water bond lengths in PyMOL

Hi Tom, Do consider that 1. the PDB format only allows four digits for residue numbers, such that water molecules must get the same number of there are more than of them. 2. periodic boundary conditions may cause water molecules to be split, making water molecules seem to miss an atom or

Re: [PyMOL] how to show PBC box?

Hi Albert, You can do: show cell Cheers, Tsjerk On Dec 7, 2016 8:44 PM, "Albert" wrote: > Hello: > > I am visualizing a MD simulation system in PyMOL. It contains the PBC > information. I am just wondering how can we show the PBC box in PyMOL? > As far as I know the

Re: [PyMOL] Starting PyMol in interactive IPython Session

Hi Leonhard, I would guess it's the formatting setting of numpy in IPython. You can see what one float really is: print(cmd.get_coords("1xyz")[0,0]) Cheers, Tsjerk On Thu, Dec 1, 2016 at 1:40 PM, Leonhard Heizinger wrote: > I guess formatting didn't work out as i

Re: [PyMOL] Scripts don't work any longer after upgrade to v1.8.4

es) > works flawlessly using v1.8.07. > > > > I will be happy about any possibly helpful suggestion. > > > > Best > > Thomas > > > > > > > > *Von:* Tsjerk Wassenaar [mailto:tsje...@gmail.com] > *Gesendet:* Donnerstag, 24. Novembe

Re: [PyMOL] Scripts don't work any longer after upgrade to v1.8.4

Hi Thomas, Can you give more information? What is in the script? Is something written in the terminal? FWIW, I have not encountered problems, and certainly not with selections. My guess is that the script breaks before getting to the selection. Cheers, Tsjerk On Thu, Nov 24, 2016 at 2:13 PM,

Re: [gmx-users] D-amino acids' force fields

; > Best regards, > > > Mijiddorj > > -- > > Message: 5 > Date: Sat, 22 Oct 2016 10:11:50 +0200 > From: Tsjerk Wassenaar <tsje...@gmail.com> > To: Discussion list for GROMACS users <gmx-us...@gromacs.org> > Subject: Re: [gmx

Re: [gmx-users] D-amino acids' force fields

Hi Mijidorj, These amino acids are chemically and topologically equivalent to their L counterparts. For united atom force fields you only need to invert the improper dihedral at the C-alpha. For atomistic force fields you don't need to change anything, except the CMAP stuff in Charmm for the

Re: [gmx-users] g_membed failure

Hi Sophia, I can't help out with mdrun -membed, but I did write a tool (insane) to avoid just the hassle you seem to face. It builds a coarse grained system, but that can be converted to atomistic. Depending on what exactly you need to do, it may be trivial or less so. In either case, if you

Re: [PyMOL] External file for writing with multiple data

Hi Daniel, Use \t in stead of \n to separate the numbers from one measurement with tabs, in stead of newlines. Do write one newline before the new series: f.write('\n') However, you might want to be a bit smarter in writing code. So you're trying to get one angle for all states?: f =

Re: [PyMOL] Placing pseudo atom on COM and saving it as pdb

ete('tmp') > > > @Tsjerk: Don't know why I got an error: Selector-Error: Invalid selection > name "pseudo". > pseudo<-- > > Thanks again for the support. > > Best Regards, > Subha > > > > > > On Wed, Oct 12, 2016 at 12:53 PM, Tsjerk Wassen

Re: [PyMOL] Placing pseudo atom on COM and saving it as pdb

Hi Subha, Probably this will get close: for pdb in open('./out').readlines(): pdb = pdb.strip() cmd.load(pdb,'tmp') cmd.pseudoatom('tmp',name='pseudo') cmd.save(pdb[:-4]+'-pseudo.pdb','pseudo') cmd.delete('tmp') cmd.delete('pseudo') ... Just a bit too much for a oneliner

Re: [gmx-users] principal component analysis chain break (Tsjerk Wassenaar)

s.org_gmx-users digest..." > > > > > > Today's Topics: > > > >1. Umbrella sampling tutorial (gozde ergin) > >2. principal component analysis chain break (??) > >3. Re: principal component analysis chain break (Tsjerk Wassenaar) > >

Re: [gmx-users] principal component analysis chain break

Ni hao Jie, The extreme projections are typically pretty meaningless. But if you want them or the more meaningful PCA output, do make sure you remove jumps over PBC from your input trajectory and have the molecules whole/clustered. Cheers, Tsjerk On Oct 7, 2016 11:21 AM, "胡杰"

[PyMOL] Leap Motion

Hey :) We've been playing recently with a Leap Motion controller for PyMol and are now wondering how we would emulate a mouse click event, based on the screen coordinates. Does anyone know? Thanks in advance, Tsjerk -- Tsjerk A. Wassenaar, Ph.D.

Re: [gmx-users] RMSD of energy minimized structure

Hi Surya, The first part ss a warning, not an error. It also says (implicitly) that if the molecules are not broken across PBC then there's nothing to worry about whatsoever. So just assert that your molecules are not split over PBC. Have a look at the trajectory. If there are frames with one

Re: [gmx-users] question

Hi Alvaro, gmx genconf Hope it helps, Tsjerk On Sep 29, 2016 4:59 PM, "ÁLVARO RODRIGO RUIZ FERNÁNDEZ" < arr...@ug.uchile.cl> wrote: > Dear gromacs users: > > How I can multiply a box full of molecules from 1x1 to 2x2 ?, I know I can > use Avogadro but in this case it does not work, I think

Re: [gmx-users] Cluster Analysis

Hi Sanket, gmx trjconv allows writing frames based on a frame index file or using a xvg file and threshold. Check the help of trjconv on it. Hope it helps, Tsjerk On Thu, Sep 29, 2016 at 9:05 AM, Sanket Ghawali wrote: > Dear, gmx-users, > > I performed a cluster

Re: [gmx-users] Problem in PCA of protein ligand system

So is there a way to extract motions of only ligand, along a particular > direction (say rotation along a dihedral in ligand) from this trajectory? > > Best Regards > Ashutosh > > On Mon, Sep 26, 2016 at 3:52 PM, Tsjerk Wassenaar <tsje...@gmail.com> > wrote: > > &g

Re: [gmx-users] Problem in PCA of protein ligand system

Hi Ashutosh, To simplify this, let's do PCA of two balls on opposite ends of a stick I'm rotating. The mean position of both ends is right at the center of rotation, and the relative positions I can describe with X and Y coordinates only. Now, the essence of PCA is the question 'which single

Re: [gmx-users] Large (600k particle) semi-isotropic lipid bilayer system transformed into vacuum-separated coordinates by grompp and mdrun

Hi George, Oh, quadrants over PBC, so it just completely ruptured. It means the area per lipid is really off in your starting structure. Where did you get it from? Cheers, Tsjerk On Sep 8, 2016 3:54 PM, "George Pantelopulos" wrote: > Dear Tsjerk and Erik, > > Thank

Re: [gmx-users] Large (600k particle) semi-isotropic lipid bilayer system transformed into vacuum-separated coordinates by grompp and mdrun

Hi George, How did you build the starting structure? The quadrants are due to distribution over cores/nodes. You can try EM on a single core for a few steps, but it seems that the system is too stretched anyway, so I think that won't really solve your problem. Cheers, Tsjerk On Sep 7, 2016

Re: [gmx-users] Odd behaviour of editconf or VMD?

Hi Jernej, This is simpler in two dimensions: Consider a hexagonal unit cell. Draw it, together with the surrounding copies (7 hexagons total). Now connect the central hexagon with the right horizontal neighbor, and with the 'northeast' neighbour. Connect these two neighbors with their other

Re: [gmx-users] X Amino Acids for Building CG Structure

Hi Elka, Methyl asparagine is not known by DSSP and is not availble in Martini. You're probably best off replacing it by asparagine: sed '/^ATOM/s/MEN/ASN/' 1HG0.pdb > out.pdb Cheers, Tsjerk On Fri, Aug 26, 2016 at 11:26 AM, Elka Firmanda wrote: > Hi, I just got "X"

Re: [gmx-users] COM-COM distance: PBC problem

Hi Arnost, When you fit with rotation the coordinates and the box are not on par anymore. Anything you do after that tries using PBC will fail. I guess that Plumed is trying to use the box to get the COM-COM distance. The only (practical) solution: don't fit. Cheers, Tsjerk On Aug 17, 2016

Re: [gmx-users] Box dimensions variation

Hi Yasser, Probably you're using semi-isotropic pressure coupling, which you should only do if you have a membrane like structure aligned with the XY plane (or a somewhat stiffish wire like structure aligned along z). Cheers, Tsjerk On Wed, Aug 10, 2016 at 3:52 PM, Yasser Almeida Hernández <

Re: [gmx-users] Magic number error in XTC file

Hi Gayathri, For the XTC file you used only a selection of atoms to write out. The TRR file always contains everything. With the conversion from TRR to XTC make sure to write the same selection as is in the other XTC files. Hope it helps, Tsjerk On Thu, Jul 28, 2016 at 7:36 AM, GAYATHRI S

Re: [gmx-users] Cutting simulatio box

y between 'single' molecule at specific 'z' of the box > indicating the phases . > > So I think my given way is easier, but not sure if the reruns goes like the > original simulations? > > > Best regards > > > On Mon, Jul 18, 2016 at 12:57 PM, Tsjerk Wassenaar <tsje...@gm

Re: [gmx-users] Cutting simulatio box

Hi Faezeh, You could use gmx select to make groups for the two phases and then perform a rerun with these new groups as energy_grps. That would give you the within and between group energies. Hope it helps, Tsjerk On Jul 18, 2016 12:49 PM, "Faezeh Pousaneh" wrote: Hi, I

Re: [gmx-users] Facing poblem in enegy minimization step

d that it might be because > either the topology is bad or the starting structure has clashes that > cannot be adequately addressed using EM or because of improper > parametrization. > > > On Sat, Jul 16, 2016 at 3:43 PM, Tsjerk Wassenaar <tsje...@gmail.com> > wrote: > >

Re: [gmx-users] Facing poblem in enegy minimization step

Hi Swagata, That's not a problem. You should be fine running a simulation, given the potential energy of the system. Check the archives for more elaborate comments on this matter. And please check the archives/google before posting questions. We like breaking our heads over new, tough issues, and

Re: [gmx-users] System blowing up in final MD run

Hi Deep, What force field? What system? How many cores? Did you try running on one? What error? Did pdb2gmx or grompp give any warnings? Cheers, Tsjerk On Wed, Jul 13, 2016 at 5:44 AM, Deep Bhattacharya wrote: > Hello, > My system is blowing up for the protein

Re: [PyMOL] ray command

Hi Mohsen, So raytracing is indeed not available in the educational version. I find this a bit strange, as I regarded the educational version the least-changed-with-respect-to-the-original (say 0.99), which did have raytracing available. Also, I like students to give me reports with pretty

Re: [PyMOL] ray command

Hi Mohsen, What happens? What error do you get? Best, Tsjerk On Jul 12, 2016 10:46 AM, "Mohsen Chitsaz" wrote: Hi Pymol users, The “ray command” is not working in my Educational version of Pymol. It seems that educational version does not allow to use this

Re: [gmx-users] Position restraints for water during EM

Hi Gregory, There is no default position restraint during EM. Of course, one wouldn't expect them to move much and one would expect the local energy minimum to be rather close to the initial position, if you used an equilibrated water box to set up the system. Cheers, Tsjerk On Jul 8, 2016

Re: [gmx-users] PCA and gmx analyze

Hi Suniba, Don't look at the cosine content. It doesn't convey anything useful. If you want to know more, I've posted more lengthy remarks about it before. Cheers, Tsjerk On Jun 27, 2016 1:11 PM, "Sun Iba" wrote: > Hello Users and experts > > My system details: > Force

Re: [gmx-users] wrap only in XZ?

Hi Albert, Rotate the system 90 degrees and use PBC in xy only. Cheers, Tsjerk On Jun 26, 2016 9:04 AM, "Albert" wrote: > Hello: > > I've got a membrane protein system and I would like the water and ions > only wrap in XZ direction. Currently, they can also wrap at Z

Re: [gmx-users] least-squares fitting the second structure on the reference structure

Hi Qasim, If you fit a trajectory, with trjconv -fit rot+trans, then each frame is fit onto the reference. Hope it helps, Tsjerk On Tue, Jun 21, 2016 at 11:12 AM, Qasim Pars wrote: > Dear users, > > From GROMACS online manual: > gmx confrms computes the root mean square

Re: [gmx-users] Insufficient memory (128 GB) for ensemble entropy calculation with gmx covar/gmx anaeig

Hi David, And why the number of frames? Cheers, Tsjerk On Tue, Jun 21, 2016 at 9:52 AM, David van der Spoel wrote: > On 21/06/16 09:40, Qasim Pars wrote: > >> Dear David, >> >> Could you please more explain each term of the formula you said? >> >> Formula=The number of

Re: [gmx-users] SOLVED: Re: helixorient, jacobi iteration or junk output...?

Hi Phil, Did you write all atoms to the trajectory or only a group? Does the reference structure match the trajectory? The Jacobi error usually occurs when there is a mismatch, and the route via a PDB file is consistent with that. Cheers, Tsjerk On Sat, Jun 18, 2016 at 3:25 AM, Phil Dude

Re: [gmx-users] Calculating Eccentricity

Hi Sanket, You probably want the clustering routine of trjconv. And then calculate the principal axes of the micelle. The instantaneous value does not mean much, but a an average non-zero eccentricity would suggest with a greater extent than without peptide would suggest an effect. Note that you

Re: [gmx-users] to neutralize the system

Hi Qasim, Not only should you neutralize the system, but you should add additional ions too. The behaviour of charged side chains which can find a partner ion from solution is different from those that can't. You won't see any problems, but the results will be affected. Not coming across any

Re: [gmx-users] Is charmm GUI ideal for membrane building

upposed to converge. Maybe you want > to verify something else? > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Tsjerk > Wassenaar <tsje...@gmail

Re: [gmx-users] Is charmm GUI ideal for membrane building

Hi Amit, What membrane and what time scale are you talking about? Complex membranes may take microseconds to equilibrate. Cheers, Tsjerk On Jun 13, 2016 06:13, wrote: > Hello everyone, > I built a lipid membrane in Charmm-GUI and tried to equilibrate it in >

Re: [gmx-users] How many times should I do Umbrella Sampling

Hi Agnivo, In addition to the remarks of Andre, if you can show that another US run on the same system gives pretty much the same result, then you can present that as proof of the robustness, and it is futile to do three more, especially if you have convergence and sufficient overlap. You can

Re: [gmx-users] Saving time of the coordinates for conformational entropy

Hi Qasim, The RMSD is not good for assessing convergence, especially if it goes above 0.5 nm. Cheers, Tsjerk On Wed, Jun 8, 2016 at 8:48 PM, Qasim Pars wrote: > Dear users, > > I have simulated a protein with simulation time of 200 ns and saving the > coordinates at

Re: [gmx-users] PCA problems

Hey :) > That usually gives a fitted ensemble that more closely retains the > original RMSD values between all pairs of structures. > This should read: ... a fitted ensemble of which the sum of the traces of all pairwise inner product matrices is closer to minimal. The pairwise RMSDs (and

Re: [gmx-users] PCA problems

Hi James, That's silly! Ambiguous means that the same structure can have multiple solutions in a fit. The fit to a single reference structure (with more than three atoms) is never ambiguous. Can never, by definition! Now if you have two reference structures at hand, and they have (quite)

Re: [gmx-users] RMSD question

Hi Teresa, You probably want to try clustering, and then check the percentage of bound/unbound structures in the clusters you get. Just the RMSD won't tell you much. Cheers, Tsjerk On Wed, Jun 8, 2016 at 11:30 AM, ingram wrote: > Dear GROMACS community, > > I am

Re: [gmx-users] PCA problems

Hi James, 'Spurious alignment' is the dependence of the resulting ensemble on the reference structure. Unfortunately, that's not solved by a progressive fit. Rather, in a progressive fit, the same configuration can have multiple orientations, based on the previous structures, which is also

Re: [gmx-users] PCA problems

Hi Teresa, No, the peptide should not be broken. Did you remove jumps over PBC? The peptide will probably be severely distorted by filtering, though. Cheers, Tsjerk On Wed, Jun 8, 2016 at 8:49 AM, ingram wrote: > Dear GROMACS community > > I am trying to complete a

Re: [gmx-users] Simulating a protein dimer

Hey :) There's a suggested workflow on the Gromacs site: http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions Cheers, Tsjerk On Jun 7, 2016 11:50 PM, wrote: > I solved the problem by using an em.tpr with pbc nojump for my dimers. pbc >

Re: [gmx-users] projection on the first two eigenvectors obtained from the concatenated trajectories

ou > said? I couldn't find anything about that on google. > > Cheers, > > On 7 June 2016 at 15:15, Tsjerk Wassenaar <tsje...@gmail.com> wrote: > > > Hi Qasim, > > > > What makes you think that they should start at 0,0 ? > > The overall mean of any s

Re: [gmx-users] DPPC-DOTAP Mixed Lipid Bilayer

Hi Nidhin, It looks like you have a version of insane that still builds oleyl with five beads. It should be four as 'CDCC' like you did for building the topology. So you also need to remove the C5 beads and shift the D to position two. Then you should be set to make/simulate your bilayers.

Re: [gmx-users] DPPC-DOTAP Mixed Lipid Bilayer

n in fibril > > structure (Md. Imrul Reza Shishir) > > 2. cannot output all the structures of one cluster (Zhenyu Meng) > > 3. Re: Non-bonded energy (ABANTIKA PAL) > > 4. Re: gmx gangle selections help (Teemu Murtola) > > 5. Re: DPPC-DOTAP Mixed Lipid Bil

Re: [gmx-users] Dodecahedron Box size and Appropriate number of SOL molecules

Hi Apramita, No restrictions. You're in charge. To get a correct density, you'll need to equilibrate with pressure coupling. Cheers, Tsjerk On Tue, Jun 7, 2016 at 1:08 PM, Apramita Chand wrote: > Hey, > Thanks a lot Tsjerk for your advice regarding box size.

Re: [gmx-users] projection on the first two eigenvectors obtained from the concatenated trajectories

Hi Qasim, What makes you think that they should start at 0,0 ? The overall mean of any set of projections lies at the origin. PCA is a pretty powerful and advanced technique, that requires quite a bit of thinking in the preparation, the execution and the interpretation. Please do read plenty of

Re: [gmx-users] Fwd: Dodecahedron Box size and Appropriate number of SOL molecules

Hi Apramita, First of all, your box diameter should be the length of the peptide plus 2, with a minimum of 2.8. Otherwise, the peptide will be able to interact directly with its periodic image. The solvent is typically added by overlaying a box of pre-equilibrated solvent and deleting all

Re: [gmx-users] DPPC-DOTAP Mixed Lipid Bilayer

Hi Nidhin, Insane allows you to build lipids from the command line. Alternatively, it's pretty easy to add DOTAP to insane, using the templates inside. If you feel you need a hand with that, let me know. Cheers, Tsjerk On Jun 7, 2016 12:21 AM, "Nidhin Thomas"

Re: [gmx-users] error installing trj_cavity with gromacs

Hi Williams, It looks like you didn't set the Gromacs include directory. What command/procedure did you use to compile? Cheers, Tsjerk On Jun 3, 2016 21:25, "Williams Miranda" wrote: > Dear GROMACS users > I use gromacs 4.6.5, then, I downloaded trj_cavity v1.1

Re: [gmx-users] allosteric effect

Hi Qasim, Do you assume MWC or KNF like allostery, and conformational based, dynamics based or mixed? Cheers, Tsjerk On Fri, Jun 3, 2016 at 2:54 AM, Qasim Pars wrote: > Dear gmx users, > > The protein I have simulated over 200 ns with GROMACS is dimer and shows >

Re: [gmx-users] Cross correlation map of residues

Hi Qasim, The plot you refer to is the result of NMA on C-alpha only. So g_covar -xpma using only C-alpha atoms should come close. You might also want to try the g_correlation tool mentioned earlier on the list, but again with a selection of only C-alpha atoms. Cheers, Tsjerk On Fri, Jun 3,

Re: [gmx-users] protonation of histidines

Hi Irem, pdb2gmx checks the hydrogen bonding network and decides which form of His fits best. Cheers, Tsjerk On Jun 2, 2016 17:20, "Irem Altan" wrote: > Hi, > > When I process a .pdb structure using pdb2gmx, how does Gromacs add > hydrogens to the histidine residues? I

Re: [PyMOL] post-processing of pdb ensemble

Hi James, This should do: for i in range(65:78): cmd.alter("bound_combined and chain %s"%chr(i+1),'chain="%s"'%chr(i)) Cheers, Tsjerk On Wed, May 25, 2016 at 5:00 PM, James Starlight wrote: > More precisely I would like to know how to script in pymol the > following

Re: [gmx-users] Using pdb2gmx with martini (coarse-grained) model to assign termini charges

Hi Sourav, For Martini there's the conversion script martinize, which has an option -nt to suppress putting charges on termini. This is not really a Gromacs question, and it's better to post Martini related questions on the forum at http://cgmartini.nl Cheers, Tsjerk On May 24, 2016 23:35,

Re: [gmx-users] find out tpx version of tpr

Hey :) If you just have the .tpr and you don't want to use Gromacs' tools, you can use python: python -c 'import struct; print "".join(struct.unpack(100*"c",open("YOUR-TPR-HERE").read(100)))' (Python 2, mind you). Cheers, Tsjerk On Mon, May 23, 2016 at 11:33 AM, Mark Abraham

Re: [gmx-users] g_cluster analysis

Hi Sapna, How should we know how many clusters you should have? A cutoff of 0.2 is quite tight, and will give many clusters. Whether that's what you want/need or whether that's meaningful/helpful for your goals is something you should consider. We don't know what you're trying or doing. Cheers,

Re: [gmx-users] WARNING no output error while dumping structures with trjconv from MD.trr

Oh, you don't want to dump one frame! You want the frames beyond 25 ns. So don't use -dump at all. You'll only get one frame though, using a spacing of 1 ns. Cheers, Tsjerk On May 21, 2016 13:53, "Tsjerk Wassenaar" <tsje...@gmail.com> wrote: > Hi Antara, > > You in

Re: [gmx-users] WARNING no output error while dumping structures with trjconv from MD.trr

Hi Antara, You indicate you want the frame at 27ns (-dump 27000), but that's not in the trajectory. The suggestion is to ask for a frame that is in, like -dump 25290 Cheers, Tsjerk On May 21, 2016 13:09, "Antara mazumdar" wrote: Dear gromacs users, I was trying to

Re: [PyMOL] a special phenomenon on using pymol

Hi Smith, You probably hit the key. Or you clicked the down triangle in the lower right menu. Cheers, Tsjerk On Fri, May 20, 2016 at 7:56 AM, Smith Liu wrote: > Dear All, > > Today as every day I do, I align 2 pdb files by pymol. After a moment, I > find the aligned 2

Re: [gmx-users] simulation_time[Nikita Bora]

Hi Nikita, It's not like there's a range to take a minimum from. It's this with this force field and that with another. Any deviation will alter the behaviour of the force field, and you'll have to show that the result is valid, either by running tests, or by referring to a paper that has results

Re: [gmx-users] Help required for calculation of protein coverage % wrt time

Hi Antara, You can also simply calculate the ratio of buried surface area to total surface area, which you can both get with gmx sasa Cheers, Tsjerk On Thu, May 19, 2016 at 3:10 PM, Sarath Chandra < sarathchandrada...@gmail.com> wrote: > You can use g_contacts tool which will give you list of

Re: [gmx-users] simulation_time

Hi Nikita, That's actually a good question, and I think it hasn't been phrased like this before. I rephrase it slightly again, so it says "which parameters should be considered part of a force field?" The first thing that springs to mind is not really a parameter, but a vital part of the force

Re: [gmx-users] Production run error

Hi Sanket, The problem is that a charge group moved too far between two domain decomposition steps. Seriously, we can't say more than that, unless you tell us more about the system and how you got to the point where you are. Cheers, Tsjerk On May 18, 2016 8:44 AM, "Sanket Ghawali"

Re: [gmx-users] Calculating Distance

Hi Sanket, You can use 'gmx traj' to write the COM over time. Cheers, Tsjerk On Wed, May 18, 2016 at 7:09 AM, Sanket Ghawali wrote: > Thank you Justin. I am sorry, I didn't make my query specific. > > g_dist calculates distance between COMS of 2 groups with

Re: [gmx-users] Removing periodic boundary condition

Hi Sanket, Can you check the structure in the tpr file (editconf -f .tpr -o .gro/.pdb)? If that is good, then -pbc nojump should work. For the second pass, you shouldn't need -pbc mol then. Cheers, Tsjerk On May 16, 2016 9:06 AM, "Sanket Ghawali" wrote: > Dear,

Re: [gmx-users] PCA and FEL

y projecting any two variables with free energy? like > RMSD and Rg? > > > Sent from my iPhone > > > On 15-May-2016, at 10:51 am, Tsjerk Wassenaar <tsje...@gmail.com> wrote: > > > > Hi Suniba, > > > > No, with gmx anaeig you can select -2d,

Re: [gmx-users] PCA and FEL

Hi Suniba, No, with gmx anaeig you can select -2d, which does a 2D projection onto the selected eigenvectors. Alternatively, you can combine any two projections onto eigenvectors, which you get using the option -proj. The quickest way to do that is something like: paste <(grep -v '^[@#]'

Re: [PyMOL] How to export secondary structure information from aPDBusing PyMol?

> > So, > L: loop > S: beta-strand > H: alpha-helix > > Is that right? > > Thank you. > > Cheng > > > -- Original -- > *From: * "Tsjerk Wassenaar";<tsje...@gmail.com>; > *Date: * Sat, May 14

Re: [PyMOL] How to export secondary structure information from a PDBusing PyMol?

\PyMOL/modules\pymol\parser.py", line > 464, in parse > exec(layer.com2+"\n",self.pymol_names,self.pymol_names) > File "", line 1, in > TypeError: int argument required > > Can I ask how to modify that? > > Thank you! > > > ---

Re: [gmx-users] (no subject)

Hi Upasana, What is your goal, your research objective? 'opening it for docking purpose' is way too vague for us to help you, other then suggesting that you are probably not choosing an optimal approach. Cheers, Tsjerk On May 14, 2016 07:04, "Upasana Ray" wrote: >

Re: [PyMOL] How to export secondary structure information from a PDB using PyMol?

Hi Zhang Cheng, If you replace SELECTION with a proper selection statement (with quotes), then something like: open("ss.dat","w").writelines( ["Residue %d: %s\n"%(a.resi,a.ss) for a in cmd.get_model(SELECTION+" and n. ca").atom] ) It will write the results to a file called ss.dat. Do mind all

Re: [gmx-users] LINCS WARNING Error in running production run in parallel of a MARTINI SYSTEM of membrane protein

Hi Antara, What commands did you use? At least make sure you add -rdd 1.6 to the command line of mdrun, because the default value is too small for coarse grain simulations. Cheers, Tsjerk On Fri, May 13, 2016 at 8:12 PM, Antara mazumdar wrote: > Dear users, > > I am

Re: [PyMOL] Contact map visualizer

Hi James, You can convert the .xpm file to .png/.jpg using tools like convert (imagemagick) and Gimp. Convert doesn't always get the Gromacs .xpm right, but it's an easy one to try. Cheers, Tsjerk On May 11, 2016 2:40 PM, "James Starlight" wrote: > Dear Pymol users! >

Re: [PyMOL] Bash scripting and pymol

Hi, You need for i in ${pdb_array[@]} do ... done Cheers, Tsjerk On Apr 27, 2016 4:44 PM, "James Starlight" wrote: > so As I tried to do it but it was not worked :-O) > > #pdbs list > pdb_array=("1UBI" "1IGD" "1G33" "1CC7" "4LGJ" "5A2H") > #where to save >

Re: [gmx-users] Higher Density than Expected

Hey :) Salt water has a higher density than pure water anyway. Cheers, Tsjerk On Apr 26, 2016 5:19 PM, "Christopher Schlicksup" wrote: > Thanks Justin. I was expecting closer to 1000kg/m^3. My reading about the > tip3p water model found approximately this value at 300K,

Re: [gmx-users] Standard volume of the simulation box

Hi Sana, There's no such thing as a standard volume. The key decision you have to take is what distance there should be between periodic images, for which the consensus view is that you need at least 2.0 nm. I typically use 2.25, corresponding roughly to 9 layers of water, so the protein can

Re: [gmx-users] question about preferred values in itp files

Hey, In addition, for Q3, sure you can have a program build you acetonitrile from the interactions. But what about cholesterol? Morphine? A protein? For just a bit more complicated stuff, let alone the really complicated stuff, you need to have coordinates to start with. Cheers, Tsjerk On Apr

Re: [gmx-users] very strange phenomenon for my production MD by gromacs

right! Cheers, Tsjerk On Apr 14, 2016 05:32, "Brett" wrote: > Dear All, > > If the issue in my production MD was caused by > "Periodic_Boundary_Conditions", I can continue my production MD until it > completed, and it will not affect my final results suppose I have it >

Re: [gmx-users] EM replicates

Hi Gregory, Yes, these steps are deterministic. Think of where the randomization should come from. Sure, there is 'random' placement of ions in genion, but it has a default seed, resulting in deterministic random numbers :) Hope it helps, Tsjerk On Apr 9, 2016 00:33, "Gregory Poon"

Re: [gmx-users] Partial density versus time

es density versus distance for different > > frames. This could be easily done by g_density with an .ndx file. I need > to > > have a plot of density-time for each of the components of the system. > > > > Please help... > > > > > > > > > > Best regards

Re: [gmx-users] Partial density versus time

actions by time? > > > > Best regards > > > On Wed, Apr 6, 2016 at 4:58 PM, Tsjerk Wassenaar <tsje...@gmail.com> > wrote: > > > Hi Faezeh, > > > > Using -b/-e flags you can get the density profile over a window of time > (or > >

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