[gmx-users] question

Dear Justin Since I want to consider the special bond between CD atom of GLU residue form peptide 1 and NZ atom of LYS residue from peptide 2, I did following steps: 1) I created 1 pdb file containing 2 peptides without any connection between aformentioned atoms (CD & NZ). I deleted OE2 atom of G

[gmx-users] martini issues

Dear all, I am learning martini method in gromacs through the tutorial http://md.chem.rug.nl/cgmartini/index.php/proteins. when solvating the system, I came across the following note: NOTE: This file uses the deprecated 'group' cutoff_scheme.

[gmx-users] Martini CG water

Dear all, I am trying to learn simulation in gromacs 5.0.4 using martini force field, when learning the tutorial (http://md.chem.rug.nl/cgmartini/index.php/proteins) step by step, I got the following note when doing gmx slovate: NOTE: This file uses the deprecated 'group' cutoff_scheme. This w

Re: [gmx-users] Dihedral copying from itp to ff

Thank you Mark, I will workout your suggestions. Regards, Raja On May 12, 2015 8:50 PM, "Mark Abraham" wrote: > Hi, > > I don't know if that particular functionality is supported, but if you look > at the way the GROMOS force fields implement their parameter lookups, you > can see that > > [dihed

Re: [gmx-users] Dihedral copying from itp to ff

Hi, I don't know if that particular functionality is supported, but if you look at the way the GROMOS force fields implement their parameter lookups, you can see that [dihedral] N C C O phi kphi mult just works, presumably by generating the default dihedraltype. You can only try [dihedral] N C

[gmx-users] gmx distance

Dear Users, I just posted a question asking about the usage. I tried myself and got the error Inconsistency in user input: Selection 'Chain_B' does not evaluate into an even number of positions (there are 475 positions) The error has been reported but how to solve I am not clear. Could anyone of

Re: [gmx-users] Dihedral copying from itp to ff

Thanks Mark, right now I am identifying the dihedral of ligand atoms in top file produced by pdb2gmx and replace the function type from default 9 to 3 and so the grompp process the new dihedral defined in the ffbonded.itp successfully. But I would like to identify a straight solution that pdb2gmx t

Re: [gmx-users] rerun under non-bonded E. terms

Great! From your last email, I thought there was no way to get what I wanted... I'll read carefully chapter 5! Cheers, Albert On 05/12/2015 02:56 PM, Mark Abraham wrote: Hi, Sorry, actually, that won't help you get non-bonded *forces* since there is no way to decompose them. You can decompo

Re: [gmx-users] Dihedral copying from itp to ff

Hi, Another way to unite two .itp files is to write a script to renumber all the atom indices in the second molecule's .itp so that they follow on from those in the first molecule. Then you can cut and paste them together. Mark On Tue, May 12, 2015 at 3:56 PM Raj D wrote: > Dear Justin, > Than

Re: [gmx-users] rerun under non-bonded E. terms

Hi, Sorry, actually, that won't help you get non-bonded *forces* since there is no way to decompose them. You can decompose energies that way. To get the forces you want, you need a .tpr that has only non-bonded interactions, and to do that correctly, you will have to explicitly list the [exclusio

Re: [gmx-users] Dihedral copying from itp to ff

Dear Justin, Thanks ,I am doing it to bring the ligand and protein under one molecule type in order to apply distance restraint between atoms of ligand and amino acids . This I am doing based on your suggestion for my earlier post https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2015-Ma

[gmx-users] calculating distances in steered dynamics

Dear Gromacs Users, I recently started using gromacs 5.0.4 for SD. I modified a few things here and there as per changes in gromacs 5.0.4. The SD ran fine. Now I want to calculate the distances from the conf0.gro file as per Justin's tutorial. I want to use the distance.pl file but i am not sure of

Re: [gmx-users] rerun under non-bonded E. terms

Thanks to you all, feel free to mark that question as "solved". Best, Albert On 05/12/2015 02:23 PM, Mark Abraham wrote: Hi, Use the nonbonded terms in the .edr files, not the totals. Mark On Tue, May 12, 2015 at 2:32 PM Albert Solernou wrote: Hi Mark, thanks for that. This was the rout

Re: [gmx-users] rerun under non-bonded E. terms

Hi, Use the nonbonded terms in the .edr files, not the totals. Mark On Tue, May 12, 2015 at 2:32 PM Albert Solernou wrote: > Hi Mark, > thanks for that. This was the route that I was taking so far. However, > and I may be missing something, I don't see how your approach excludes > the bonded t

Re: [gmx-users] first residue in chains warning issue

Thanks. EM and NPT run without any warnings. Sent from my Huawei Mobile Justin Lemkul wrote: On 5/12/15 8:10 AM, Ming Tang wrote: > > Thanks Justin, > > At first, I wanted to choose NONE in for both N and C terminus, but it gave > me the same warnings for both the first and the last residue

Re: [gmx-users] rerun under non-bonded E. terms

Hi Mark, thanks for that. This was the route that I was taking so far. However, and I may be missing something, I don't see how your approach excludes the bonded terms from the -rerun calculation. Thanks, Albert On 05/12/2015 01:16 PM, Mark Abraham wrote: Hi, This is one of the things for w

Re: [gmx-users] first residue in chains warning issue

On 5/12/15 8:10 AM, Ming Tang wrote: Thanks Justin, At first, I wanted to choose NONE in for both N and C terminus, but it gave me the same warnings for both the first and the last residue in every chains. However, choose NH3+/COO- and NH2/COOH just gave that warning for the first residue.

Re: [gmx-users] rerun under non-bonded E. terms

Hi, This is one of the things for which mdrun -rerun on a subset trajectory is useful. Make the subset trajectory, make the subset topology (including keeping bonds plus their associated exclusions, as appropriate) and you'll get the forces. tpbconv can make subsets, but YMMV. Mark On Tue, May 1

Re: [gmx-users] rerun under non-bonded E. terms

Hi, I may have not expressed well my final goal. I need a trajectory, a .trr file, that has the forces. I am interested in the non-bonded forces of a sub-set of the residues, so I need to re-compute these, and cannot use the values that come from the full trajectory where all the residues are

Re: [gmx-users] first residue in chains warning issue

Thanks Justin, At first, I wanted to choose NONE in for both N and C terminus, but it gave me the same warnings for both the first and the last residue in every chains. However, choose NH3+/COO- and NH2/COOH just gave that warning for the first residue. The angles and bonds in .itp are like t

Re: [gmx-users] rerun under non-bonded E. terms

On 5/12/15 7:57 AM, Albert Solernou wrote: Thanks Justin, still I would not know how to go from a .edr file into a trajectory that has the forces of the atoms I am interested in. You don't. The .edr file is the energy output of a simulation. If you have your subtrajectory of interest, you

Re: [gmx-users] rerun under non-bonded E. terms

Thanks Justin, still I would not know how to go from a .edr file into a trajectory that has the forces of the atoms I am interested in. Best, Albert On 05/12/2015 12:48 PM, Justin Lemkul wrote: On 5/12/15 7:46 AM, Albert Solernou wrote: Well, back to the beginning, then. Is there a way t

Re: [gmx-users] rerun under non-bonded E. terms

On 5/12/15 7:46 AM, Albert Solernou wrote: Well, back to the beginning, then. Is there a way to do a re-run using only non-bonded energy terms? I'll explain a bit further. I have a trajectory, and want to get a (sub)trajectory that has only a sub-set of atoms and that accounts only for the non

Re: [gmx-users] rerun under non-bonded E. terms

Well, back to the beginning, then. Is there a way to do a re-run using only non-bonded energy terms? I'll explain a bit further. I have a trajectory, and want to get a (sub)trajectory that has only a sub-set of atoms and that accounts only for the non-bonded interactions within this sub-set of

Re: [gmx-users] Protein+ligand complex

On 5/12/15 7:41 AM, Kashif wrote: Greetings of the day, Can I use nvt.mdp and npt.mdp parameter file given in tutorial ( http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex_old/index.html) for my 5 ns production run? As the tutorial shows 100 ps nvt and npt equilibr

Re: [gmx-users] all-atom pca

Hi Tsjerk I think am lost now when you say 'filtered' which I don't know what it means. Manual says: -proj : calculate projections of a trajectory on eigenvectors -extr : calculate the two extreme projections along a trajectory on the average structure Saying that analysis done on heavy atoms a

[gmx-users] Protein+ligand complex

Greetings of the day, Can I use nvt.mdp and npt.mdp parameter file given in tutorial ( http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex_old/index.html) for my 5 ns production run? As the tutorial shows 100 ps nvt and npt equilibration and 1000 ps (1 ns) MD Simulation

Re: [gmx-users] first residue in chains warning issue

On 5/11/15 6:48 PM, Ming Tang wrote: Hi Justin, Here is the output of pdb2gmx: Command line: pdb2gmx -f hyp_lys.pdb -o complex.gro -ignh -ter -ff gromos54a7 -water SPC Using the Gromos54a7 force field in directory gromos54a7.ff Opening force field file /usr/local/gromacs/share/gromacs/

Re: [gmx-users] LINCS warnings and ligand topology

On 5/11/15 9:07 PM, MPI wrote: Hi Justin, Thanks for your suggestions. Hacking off atoms because the simulation fails is a pretty bad strategy :) Indeed, I removed all O atoms and S atom. Simulations in solvent are perfectly fine. This might suggest that the errors (warnings) came direct

Re: [gmx-users] Dihedral copying from itp to ff

On 5/12/15 12:05 AM, Raj D wrote: Dear User, I have done MD simulation successfully with ligand.itp file produced by Antechamber. Now I have to include the ff information of the ligand into AMBER99SB forcefield and in the process I am so for successful in creating rtp entry and bond and angles

Re: [gmx-users] question

On 5/12/15 12:36 AM, Andrew Bostick wrote: Dear Justin Very thanks for your answer I should use my pdb file in which there is no bond between CD atom of GLU residue from peptide 1 and NZ atom of LYS residue from peptide 2. Creating new entry in specbond.dat file will consider this new bond. I

Re: [gmx-users] rerun under non-bonded E. terms

On 5/12/15 6:58 AM, Albert Solernou wrote: Hi, I am getting fairly large values for the LJ energy term (order 10^8), while previous values were much better (order 10^5). I am wondering whether there is a radius decrease for bonded atoms or something equivalent to explain these differences. I br

Re: [gmx-users] rerun under non-bonded E. terms

Hi, I am getting fairly large values for the LJ energy term (order 10^8), while previous values were much better (order 10^5). I am wondering whether there is a radius decrease for bonded atoms or something equivalent to explain these differences. I browsed quickly the manual but could not fin

[gmx-users] Gromacs 5.0.4 with Gaussian09 QM/MM interface

Dear All, I'm intending to perform QM/MM calculations with Gromacs 5.0.4 and Gaussian09. As I understand I need to make modifications in some Gaussian files. I've found instructions for that (http://wwwuser.gwdg.de/~ggroenh/roadmap.pdf) but they consider Gaussian03. Can someone write me what mod

Re: [gmx-users] Can't load converted trajectory on to vmd

Hi, As the VMD documentation probably says somewhere, you can't load a trajectory into a molecule with a different number of atoms. So make a gro file that matches the atom number and ordering of your trajectory, e.g with trjconv. Mark On Tue, 12 May 2015 10:32 Seera Suryanarayana wrote: > Dea

[gmx-users] Can't load converted trajectory on to vmd

Dear gromacs users I have executed the trjconv command for generating the .xtc file to futher analysis. I have selected protein for output. I loaded the .gro file on to vmd and then I tried to load .xtc file on to vmd. But, I couldn't load it and I got the following error. vmd > Info) Using plug