Re: [gmx-users] issue regarding gromacs software

I do not see the attachment... Which forcefield are planning to use? In any case you should check the input pdb you are using: are the amino acid residues named in the proper way? It is a standard pdb? Do you have some non-natural amino acid or modified residue in your peptide? Moreover you

Re: [gmx-users] Obtaining opls forcefield

; > have a look maybe helpful if your molecule is hydrocarbon > http://zarbi.chem.yale.edu/ligpargen/ > > > >> On Tue, Feb 12, 2019 at 9:54 AM Valerio wrote: >> >> Dear all, >> >> I have been trying to obtain opls forcefield for small molecules. &g

[gmx-users] Obtaining opls forcefield

in combination with ffconv.py script to generate the topology. Unfortunately the link for the ffconv.py link is expired and it is not possible to download it anymore. Can someone please send me the script or mailing me the code? Thanks a lot in advance. Valerio -- Gromacs Users mailing list

[gmx-users] Obtaining opls forcefield

and it is not possible to download anymore. Can someone please send me the script or mailing me the code? Thanks a lot in advance. Valerio -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post

[gmx-users] Obtaining opls forcefield

and it is not possible to download anymore. Can someone please send me the script or mailing me the code? Thanks a lot in advance. Valerio -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post

[gmx-users] H-bond analysis

). I have also tried to calculate just the number and perform the calculation with gmx analyze using the -luzar option but again I have segmentation fault... Can anyone tell me if I am doing something wrong and how to follow the right procedure? Thanks a lot in avvance. Valerio Ferrario

Re: [gmx-users] gmx analyze Luzar analysis

analysis... Reducing the time I obtain the same relaxation values With better integrals: Hydrogen bond thermodynamics at T = 300 K One-way 0.030 33.376 13.321 Integral 0.085 11.729 10.713 Relaxation 1.038 0.963 4.478 Valerio 2017-08-29 14:01 GMT+02

[gmx-users] gmx analyze Luzar analysis

Dear all, I am trying to obtain parameters for h-bonds. I used the tool gmx hbonds with -ac option but resulted in segmentation fault. Therefore from the normal gmx hbond output I used gmx analyze to obtain the autocorrelation function. Therefore, using again gmx analyze with -luzar options and

Re: [gmx-users] gmx spatial

. Moreover the trajectory seems very good, with the protein perfectly superposed and with the same orientation in each trajectory step. Is there a way to define the interaction? i.e. the 2 selected groups interacts when they are within a given distance? Best, Valerio 2017-06-28 3:29 GMT+02:00 Dallas

[gmx-users] gmx spatial

that the density should be just around the protein (in this case). Moreover I have just positive values for the isosurface, is that normal? Am I doing something wrong? Thanks a lot, Valerio Ferrario -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX

[gmx-users] Help for gmx enemat

Hi Justin, I need the LJ potential just between the two DNAs, instead gmx energy calculates the total LJ energy. Is it right? Valerio Il giovedì 14 gennaio 2016, Justin Lemkul <jalem...@vt.edu <javascript:_e(%7B%7D,'cvml','jalem...@vt.edu');>> ha scritto: > > > On 1/14/16

Re: [gmx-users] Help for gmx enemat

Hi Justin, You are right!! Thanks a lot!! Your help was precious. Again thanks. Valerio 2016-01-14 18:26 GMT+01:00 Justin Lemkul <jalem...@vt.edu>: > > > On 1/14/16 12:18 PM, valerio di giulio wrote: > >> Hi Justin, >> >> I need the LJ potential just betw

[gmx-users] Help for gmx enemat

elements Last energy frame read 500 time 500.000 Will build energy half-matrix of 2 groups, 0 elements, over 501 frames Segmentation fault (core dumped) ... Although I have written to the .mdp file: energygrps = DNA1 DNA2 Thank you in advance, Valerio Di Giulio -- Gromac

Re: [gmx-users] Help for gmx enemat

tp" ; Include generic ion topology #include "amber03.ff/ions.itp" [ system ] Two all-AT in water [ molecules ] DNA11 DNA21 SOL 39390 NA 190 CL 146 . Thanks, Valerio 2016-01-13 20:40 GMT+01