[gmx-users] order of atom indices regarding proper dihedrals

hi folks, i'm a little stuck in the question whether the order of atom indices (a1-a2-a3-a4 or a4-a3-a2-a1) plays any role when defining an additional/new proper dihedral. as usual, i utilize the amber99sb force field. for the computation of the potential, the order shouldn't play any role,

Re: [gmx-users] terminal phosphate residue for dna simulations

DT, DC, DG). You just have to consider your terminal nucleotides as regular ones (i.e. named as DA instead of DA3 or DA5 and so on). More details you can find in my paper: doi: *10.1021*/*jp1035663* * * Best regards Paulo Netz On Tue, Feb 19, 2013 at 10:35 AM, Vedat Durmaz wrote: hi guys, does

[gmx-users] terminal phosphate residue for dna simulations

hi guys, does anyone know about a way to simulate mono- or polynucleotides along with a 3' or 5' bound monophosphate using an amber force field like ffamber99sb? i couldn't find any residue definition for a terminal phosphate group such as " P3' " or " P5' " (exemplarily). do they indeed not

Re: [gmx-users] merge .gro, .top files

there's also an executable topology merger available written in python called "gromacs_topology_merger.py" as part of a the software package "ZIBMolPy" designed for conformational analysis at https://github.com/CMD-at-ZIB/ZIBMolPy given (in the same directory) a topology file "topol.top" (argu

Re: [gmx-users] missing gbsa parameters

before Protein_*.itp line in /Complex.top/. Are you inserting your gbsa.itp in the *right* place of your top file? Alan On 4 May 2012 14:14, Vedat Durmaz <mailto:dur...@zib.de>> wrote: thanks justin and alan. i also had the suspicion that the error is caused by case

Re: [gmx-users] missing gbsa parameters

bout 10 ARE listed in gbsa.itp. any idea what might cause that? Am 04.05.2012 15:26, schrieb Justin A. Lemkul: On 5/4/12 9:14 AM, Vedat Durmaz wrote: thanks justin and alan. i also had the suspicion that the error is caused by case sensitivity. simply replacing all atom types from

Re: [gmx-users] missing gbsa parameters

idea? is there perhaps some other force field/database file that is checked apart from gbsa.itp?! thanks again, vedat Am 04.05.2012 11:23, schrieb Alan: Hi there, look at 'acpype -h', in particular: -g, --disambiguatedisambiguate lower and uppercase atomtypes in GMX top

[gmx-users] missing gbsa parameters

ne that can tell me how (with which parameter values) to add GAFF atom types like e.g. "ss", "hn", "hx", "os" to the gbsa.itp file? thanks in advance and take care vedat durmaz -- gmx-users mailing listgmx-users@gromacs.org http://list

Re: [gmx-users] PBC - Protein and Ligands

i always did it (successfully) with one single command: trjconv -f md.trr -s md.tpr -o mdCompact.trr -pbc mol -ur compact -n ../../index.ndx regards vedat Am 29.02.2012 18:01, schrieb Steven Neumann: Dear Gmx Users, I am run a simulation with Gromacs 4.5.4. of my protein and 15 ligands. T

Re: [gmx-users] using g_angle

hi francesca, i think what you are looking for is this g_sgangle $indexFile -f $traj -s $tpr -oa $outfile before that, you have to define two planes (by 3 atom indices each) in your index file [ dihed1 ] 523 680 3482 [ dihed2 ] 680 3482 3691 which you choose when having started g_sgangle.

Re: [gmx-users] Implicit solvent - Gromacs 4.5.4

Number of steps = 3 Step Time Lambda 0 0.0 0.0 　 Steepest Descents converged to Fmax < 1000 in 1 steps Potential Energy = inf Maximum force = 0.000e+00 on atom 0 Norm of force = nan Can you please explain? Steven On Tue, Feb 28, 2012 at 2:29 PM, Ved

Re: [gmx-users] Implicit solvent - Gromacs 4.5.4

thanks justin for clearing up these issues .. Am 28.02.2012 15:50, schrieb Justin A. Lemkul: Vedat Durmaz wrote: actually, as far as i know, the -DFLEXIBLE argument has no effect on simulations without explicit water ?! The #ifdef FLEXIBLE block does only affect explicit water

Re: [gmx-users] Implicit solvent - Gromacs 4.5.4

arning. A system that is unstable will cause the LINCS algorithm to fail, but turning off constraints does not prevent a system from becoming unstable or crashing. -Justin Also thanks Vedat for sharing, Best regards, Steven On Tue, Feb 28,

Re: [gmx-users] Implicit solvent - Gromacs 4.5.4

hi steven, i've been simulating a 33 AA peptide for the past two days using implicent solvent in order to achieve a proper folding. i haven't added counterions, however, the systems shows nice results according to what i've expected. the mdrun command (for the extension) for our hardware lo

Re: [gmx-users] certain number of solvent molecules with genbox WITHOUT "ci"/"nmol" options

thanks to you two, mark & justin! that's it ... -maxsol was the keyword for this problem. (which i actually could have found it myself if having looked carefully after typing "genbox -h") Am 09.01.2012 13:57, schrieb Mark Abraham: On 9/01/2012 11:24 PM, Vedat Durmaz wro

Re: [gmx-users] certain number of solvent molecules with genbox WITHOUT "ci"/"nmol" options

Am 09.01.2012 12:37, schrieb Mark Abraham: On 9/01/2012 9:00 PM, Vedat Durmaz wrote: hi guys, i have a molecular system that i want to simulate many times with differing initial conditions, but each with the same number of (solvent) atoms! i'm using gromacs 4.5.4 ... Use different v

[gmx-users] certain number of solvent molecules with genbox WITHOUT "ci"/"nmol" options

hi guys, i have a molecular system that i want to simulate many times with differing initial conditions, but each with the same number of (solvent) atoms! i'm using gromacs 4.5.4 ... genbox with "-cs" gives me different numbers of solvent molecules. putting more than 20,000 tip4p molecules w

Re: [gmx-users] potential energy of one molecule using GAFF: confused regarding Ryckaert-Bellemans and 1-4 potentials

Am 20.10.2011 15:01, schrieb Mark Abraham: On 20/10/2011 7:25 PM, Vedat Durmaz wrote: thanks mark. i guess it took some time answering all these questions. and i think you are right. trying to interpret each computed energy term seperately in a physical manner is senseless. especially since

Re: [gmx-users] potential energy of one molecule using GAFF: confused regarding Ryckaert-Bellemans and 1-4 potentials

thanks mark. i guess it took some time answering all these questions. and i think you are right. trying to interpret each computed energy term seperately in a physical manner is senseless. especially since i'm not really deep inside the force field & implementation stuff. however, with one of

[gmx-users] potential energy of one molecule using GAFF: confused regarding Ryckaert-Bellemans and 1-4 potentials

ctive potentials are modified in such various ways among the force fields? Q8 does anyone have an idea, how to perform the simulation and on which energy terms to concentrate in order to get reliable results? thanks in advance and sorry for the long text ... as i've already told you

Re: [gmx-users] Re: acetonitrile from amber to gromacs

hi alan and all others, i love it. i've probably never seen such a helpful and constuctive answer to a question asked over the gmx user mailing list. following your instructions was very informative on the one hand and provided the results that i needed on the other. slightly modifying the the c

Re: [gmx-users] Re: acetonitrile from amber to gromacs

Alan schrieb: > Dear Vedat, > > On Wed, May 19, 2010 at 20:36, > wrote: > > @rui > acpypi -i ch3cn_210.pdb > says: "cannot find template for residue C3N in our library". and > indeed, > there's no residue C3N in my ffamber99sb.rtp file >

Re: [gmx-users] acetonitrile from amber to gromacs

mber99sb.n2t not found in current dir nor in your GMXLIB path". there are n2t files, but not for the amber ff. what have i done wrong? > I did it for other solvent. If you have AMBER is very easy to do. Do > you have AMBER? > > On Wed, May 19, 2010 at 12:15 PM, vedat durmaz wrote:

[gmx-users] acetonitrile from amber to gromacs

hi all together, this week i'm trying to do some simulations with acetonitrile (AN) as a solvent and using ffamber99 as force field. on this website http://www.pharmacy.manchester.ac.uk/bryce/amber#box i found a gorgeous little box containing a pretty number of 6-site modeled AN molecules, repr

Re: [gmx-users] suitable parameter settings for intermolecular non-bonded interaction

Mark Abraham schrieb: > On 31/03/2010 11:44 PM, vedat durmaz wrote: >> thanks to both of you for your helpful hints. actually, i'm not using >> the LIE method as available with the gromacs package, but planning to >> implement the model myself using energies from grom

Re: [gmx-users] suitable parameter settings for intermolecular non-bonded interaction

> On 31/03/2010 9:15 PM, vedat durmaz wrote: >> hello out there, >> >> i'm trying to simulate a receptor ligand system in order to extract >> intermolecular non-bonded interaction energies (vdw/coulomb) and apply >> the linear interaction energy model. >

[gmx-users] suitable parameter settings for intermolecular non-bonded interaction

hello out there, i'm trying to simulate a receptor ligand system in order to extract intermolecular non-bonded interaction energies (vdw/coulomb) and apply the linear interaction energy model. which parameter settings do you recommend for highly accurate results? up to now, i had chosen (copied f

Re: [gmx-users] query regarding atom type

hi there, i'm doing simulation of protein-ligand systems since a few weeks and i've been starting with a nice tutorial for acpypi (python script) http://code.google.com/p/acpypi/wiki/TutorialAcpypi4Gromacs in order to create topology-files for several (42) ligands in an automized way. works very

[gmx-users] omit solvent's coordinates in output file

dear gromacsters, does anyone know a way to tell gromacs which molecule's coordinates to write to the output file which should be as small as possible? i don't need the solvent's coordinates for example. starting run like: grompp -f ../../md.mdp -c eq.gro -n index.ndx -p complex.top -o md.tpr mp

[gmx-users] g_hbond output

hi out there, still doing my first steps on the gmx planet. can anyone tell me, why there are 3 columns in the output file of g_hbond and how to interpret the output values when having run g_hbond -f mdNew.xtc -s md.tpr -num mdNew_numH.xvg first column frame! second column = #H bonds? third colu

Re: [gmx-users] editconf/genbox: molecular complex outside simulation box

thanks. things are getting clearer and life's going a little easier, now. Justin A. Lemkul schrieb: > > > dur...@zib.de wrote: >> hi there, >> >> it's my first steps with gromacs and i can't get rid of the following >> problem: >> >> i set up my box with >> >> editconf -bt dodecahedron -f complex

[gmx-users] editconf/genbox: molecular complex outside simulation box

hi there, it's my first steps with gromacs and i can't get rid of the following problem: i set up my box with editconf -bt dodecahedron -f complex.pdb -o complex.pdb -c -d 0.9 and fill it up with water like genbox -cp complex.pdb -cs ffamber_tip3p.gro -o outfile.pdb -p complex.top but when vi