[gmx-users] sampling the side chain conformations by MD simulations

Dear All: I am conducting molecular dynamics simulations of a proetin. The side chain conformation of one key residue is important for the protein function and I wang to sampling its conformations and calculate the energy barrier when it changes between different conformations. However, the c

Re: [gmx-users] gromacs 4.5.5 on Cygwin

On 22/04/2012 9:30 AM, vijaya subramanian wrote: Hi I am trying to install gromacs 4.5.5 on cygwin following the instructions in the wiki. I first installed fftw3 using the following commands: ./configure --enable-float make make install I then tried installing gromacs using: ./configure --dis

Re: [gmx-users] Fwd: help

On 22/04/2012 2:02 AM, vineetha mandlik wrote: -- Forwarded message -- From: *vineetha mandlik* > Date: Sat, Apr 21, 2012 at 9:22 PM Subject: help To: gmx-users-requ...@gromacs.org Respected Sir/Madam I am n

[gmx-users] gromacs 4.5.5 on Cygwin

Hi I am trying to install gromacs 4.5.5 on cygwin following the instructions in the wiki. I first installed fftw3 using the following commands: ./configure --enable-float make make install I then tried installing gromacs using: ./configure --disable-threads as well as ./configure --disable-th

Re: [gmx-users] fatal error: The solvent group non-Protein is not continuous

On 4/21/12 1:17 PM, Shima Arasteh wrote: Dear gmx users, I am a new user of gromacs. I solvated my protein in water. Now I want to neutralize the system. I added 2 CL ions to the system but when run the following command, get the fatal error: # genion -s ions.tpr -o monomer_solv_ions.gro -p

Re: [gmx-users] Error: No default angle/bond types

On 4/21/12 12:07 PM, Shima Arasteh wrote: Dear gmx users, When I enter the grompp command, I get this fatal error. How can I solve its problem? # grompp -f ions.mdp -c monomer_solv.gro -p topol.top -o ions.tpr The error will print out the offending line, which you can use to find which at

[gmx-users] where can we obtain the latest Amber ff12SB FF?

hello: I am wondering where can we obtain the latest Amber ff12SB FF for Gromacs? thx -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Pleas

Re: [gmx-users] Fwd: help

HI vineetha, On Sat, Apr 21, 2012 at 9:32 PM, vineetha mandlik wrote: > > > > > > Respected Sir/Madam > > I am new to gromacs and on giving the grompp command after genion command > I am getting the following error: > > > > Even after running the genion command and adding 4 Na+ ions before the >

[gmx-users] fatal error: The solvent group non-Protein is not continuous

Dear gmx users, I am a new user of gromacs. I solvated my protein in water. Now  I want to neutralize the system. I added 2 CL ions to the system but when run the following command, get the fatal error: # genion -s ions.tpr -o monomer_solv_ions.gro -p topol.top -nname CL -nn 2 fatal error: Th

[gmx-users] Error: No default angle/bond types

Dear gmx users, When I enter the grompp command, I  get this fatal error. How can I solve its problem? # grompp -f ions.mdp -c monomer_solv.gro -p topol.top -o ions.tpr Thanks in advance, Shima -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-use

[gmx-users] Fwd: help

-- Forwarded message -- From: vineetha mandlik Date: Sat, Apr 21, 2012 at 9:22 PM Subject: help To: gmx-users-requ...@gromacs.org Respected Sir/Madam I am new to gromacs and on giving the grompp command after genion command I am getting the following error: Even after running

Re: [gmx-users] Type of unit cell

On 22/04/2012 1:13 AM, Shima Arasteh wrote: So I can not change the type of unit cell in regenerating a job done before, right? You can't replicate the simulation (see, for example, http://www.gromacs.org/Documentation/Terminology/Reproducibility). You can attempt to replicate the observation

Re: [gmx-users] Type of unit cell

So I can not change the type of unit cell in regenerating a job done before, right? Cheers, Shima From: Mark Abraham To: Discussion list for GROMACS users Sent: Saturday, April 21, 2012 7:23 PM Subject: Re: [gmx-users] Type of unit cell On 22/04/2012 1

Re: [gmx-users] Type of unit cell

On 22/04/2012 12:00 AM, Shima Arasteh wrote: Dear Gomacs friends, I'd like to know if it makes different in the last outcomes of a simulation when I change the box? Yes, it changes. For example I use dodecahedron instead of cubic one. I just know that I need to add less numbers of water mol

[gmx-users] Type of unit cell

Dear Gomacs friends, I'd like to know if it makes different in the last outcomes of a simulation when I change the box? For example I use dodecahedron instead of cubic one. I just know that I need to add less numbers of water molecules. Thanks in advance, Shima -- gmx-users mailing listgmx

Re: [gmx-users] Charm forcefield error..Atomtype CR not found ..

Hi Gromacs Friends, Thank you mark for your solution . Sorry for my incomplete information on topic.. The CR atom type in ligand corresponds to the cyclohexane atoms in the ligands... I think I have to change the CR name , but what should be the new name With Best Wishes, David On Sat,

Re: [gmx-users] Charm forcefield error..Atomtype CR not found ..

On 21/04/2012 9:27 PM, rama david wrote: Hi Gromacs Friends, I wish to apply charmff 27 to my protein and ligand I proceed in following way .. 1. I separate the protein and ligand by grep command then delete the ligand lne grom pdb file 2 I generate the topology of protein in gromacs

Re: [gmx-users] using AMBER force field by GROMACS

On 21/04/2012 9:23 PM, Acoot Brett wrote: Dear All, By gromacs pdb2gmx, we can choose the amber force field. Suppose we have chosen the amber force field, now let us see add ions. By gromacs command "genion -s ions.tpr -o solv_ions.gro -p topol.top -pname NA -nname CL -neutral -conc 0.1", besi

[gmx-users] Charm forcefield error..Atomtype CR not found ..

Hi Gromacs Friends, I wish to apply charmff 27 to my protein and ligand I proceed in following way .. 1. I separate the protein and ligand by grep command     then delete the ligand lne grom pdb file 2  I generate the topology of protein in gromacs     using the pdb2gmx command 3   I generate the

[gmx-users] using AMBER force field by GROMACS

Dear All,   By gromacs pdb2gmx, we can choose the amber force field. Suppose we have chosen the amber force field, now let us see add ions.   By gromacs command "genion -s ions.tpr -o solv_ions.gro -p topol.top -pname NA -nname CL -neutral -conc 0.1", besides neutralize the system, we also add 0