[gmx-users] possible buckingham potenital bug!

gmx-users，您好！ i have added bucking ham for the nonbonded interactions, and no L-J nobonded are used together with the buckingham parameters,as i read from the mailing list that mixed use of buckingham and L-J are not supported by the neighbor searching algorithm. but when genpa

Re: [gmx-users] Including water in for restraining

Hi Chris, Thanks for your effort to write me the detailed reply. In fact I tried to put harmonic restraint to one water molecule bound on Zn2+ within the active site of protein of my interest. The crystal structure reports four ligating atoms with Zn2+, in addition to H20; other three are from two

[gmx-users] Including water in for restraining

While I am using harmonic restraint for water and Zn, I am unable to do so since the chain A "itp" file does not contain water, It shows error as follow --- Program grompp, VERSION 3.3.1 Source code file: toppush.c, line: 1108 Fatal error: [ file

[gmx-users] Including water in for restraining

Hi gmxions, While I am using harmonic restraint for water and Zn, I am unable to do so since the chain A "itp" file does not contain water, It shows error as follow --- Program grompp, VERSION 3.3.1 Source code file: toppush.c, line: 1108 Fatal

[gmx-users] g_density for a micelle

Does anybody have a modified g_density for calculation from the center of mass of a micelle? Thanks. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the

Re: [gmx-users] protonated cys -S

Giacomo Bastianelli wrote: This is the matrix that I obtain. CYS1CYS1CYS5CYS5VAL6 CYS10 CYS10 N1 SG4 N27SG30 C38 N55SG58 CYS1 SG4 0.302 CYS5 N27 0.988 0.900 CYS5SG3

Re: [gmx-users] RESP fitting using MOPAC

Hi Ran, Thanks for your suggestion. B.Nataraj On Fri, 10 Nov 2006 09:16:29 +0100, "Ran Friedman" <[EMAIL PROTECTED]> said: > Hi, > > The setting of partial charges is a delicate matter. How you do it > depends on your ligand, the force-field you use and computational power > available to you. If

Re: [gmx-users] protonated cys -S

This is the matrix that I obtain. CYS1CYS1CYS5CYS5VAL6 CYS10 CYS10 N1 SG4 N27SG30 C38 N55SG58 CYS1 SG4 0.302 CYS5 N27 0.988 0.900 CYS5SG30 1.070 0.917 0.333

Re: [gmx-users] pdb2gmx with force field option

Mohamed Osman a écrit : As my first Gromacs simulation I am trying to simulate a protein with K+ ion. When I use pdb2gmx with GROMACS96 43a2, it complains about the K+ ion and does not generate the topology file. When I remove the K+ ion, I get a topology file, but I need the K+ for the simu

Re: [gmx-users] protonated cys -S

Try renaming the Cys in the the PDB to CYS2. Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mp

Re: [gmx-users] protonated cys -S

Giacomo Bastianelli wrote: Hi Tsjerk, the distance of the "not formed" S-S is 0.202 while the two "formed" S-S are 0.204 and 0.203. Therefore, gromacs should recognize all three and create the SS bonds. CYSSG1CYSSG10.2CYS2CYS2 this is the second line of my specb

Re: [gmx-users] protonated cys -S

Hi Tsjerk, the distance of the "not formed" S-S is 0.202 while the two "formed" S-S are 0.204 and 0.203. Therefore, gromacs should recognize all three and create the SS bonds. CYSSG1CYSSG10.2CYS2CYS2 this is the second line of my specbond.dat Thanks, Giacomo T

[gmx-users] RE. pdb2gmx with force field option (Mohamed Osman)

jagshemash (hi) Mohammed, OK there are two ways of dealing with this: 1. You add water with genbox run grommpp ..then feed in the resulting *tpr file into genion...genion replaces a water molecule with a pre-selected appropriate ion ("genion -h" should give you the help menu). However, you mus

Re: [gmx-users] protonated cys -S

Hi Giacomo, The two sulphur atoms have to be at a proper distance to be recognized as involved in a S-S bond. In your case, if you're certain that there should be a bond, you have to edit the file specbond.dat, find the entry which links two cysteine residues and set the distance to the actual di

[gmx-users] protonated cys -S

Dear users, I have just found that gromacs protonate the -S of my Cys and I would like to have it deprotonated to form a disulphide bond (It is present in the original pdb file). Is there any way I can modify it? thanks in advance, Giacomo ___ gmx-us

Re: [gmx-users] Problem in setting rlist, rcoulomb

nur avneet wrote: for my run...the terminal gives an error as: "the cut off length is longer then half the shortest box vector or longer then the smallest box diagonal element. Increase the box size or decrease the rlist." Actually this error message is from grompp and it means what it says.

[gmx-users] Problem in setting rlist, rcoulomb

When I set the  *.mdp file as follows:  ; Steepest escent in vacuo ; hyb2a ; ; Input File ; cpp = /usr/bin/cpp constraints = none integrator = steep nsteps = 500 ; ; Energy minimising stuff ; emtol = 1000 emstep = 0.01 nstcomm = 1 ns_type = grid morse = no coulombtype = Shift vdw_type = Shift rlis

Re: [gmx-users] RESP fitting using MOPAC

Hi, The setting of partial charges is a delicate matter. How you do it depends on your ligand, the force-field you use and computational power available to you. If you're just simulating a single protein, than I would use an ab-initio of DFT potential rather than semi-empirical one such (which is