[gmx-users] regarding error in editconf

Dear friends when I am trying command editconf, it is showing error File input/output error I have protein of 700 amino acids and its of inverted T shape and we are giving boxtype dodecahedron. input command is: editconf_d -bt dodecahedron -f input.gro -o box.gro -c -d 10.0 with regard

RE: [gmx-users] charmm27 force filed bug for MET residue with vsites in gromacs 4.5.2

Hi, Note that grompp prints the atomtype that causes the problems. You should copy the last line of share/top/charmm27.ff/gb.itp and rename MCH3 to MCH3S. I have fixed this for 4.5.3 and I have also made the grompp error messages clearer. Berk From: zhn...@gmail.com To: gmx-users@gromacs.org

[gmx-users] GB-polarization

Dear all, I've got a general question regarding implicit solvent simulations. Using g_energy there's an option to print out the GB-polarization. Is that the solvent-solute electrostatics polarization free energy? How can one interpret a rise or decrease in the GB-polarization? Kind regards,

[gmx-users] g_sas resarea.xvg

Hi everyone, I used g_sas: g_sas -s .tpr -f .xtc -n .ndx -o .xvg -or resarea.xvg What I don't understand is why there are 3 columns in the file resarea.xvg although this is what's written in my file: # g_sas is part of G R O M A C S: # # GROtesk MACabre and Sinister # @title "Area per residue

Re: [gmx-users] g_hbond

Hi Erik, I tried what you said: I made index groups containing only the atoms involved in that hbond and ran g_hbond again. The problem didn't persist. So I wanted to check if I misinterpreted the map: for that, I compared my 4 index files: the one of my concatenated trajectory and the three of th

Re: [gmx-users] regarding error in editconf

Anamika Awasthi wrote: Dear friends when I am trying command editconf, it is showing error File input/output error I have protein of 700 amino acids and its of inverted T shape and we are giving boxtype dodecahedron. input command is: editconf_d -bt dodecahedron -f input.gro -o box

Re: [gmx-users] g_sas resarea.xvg

Carla Jamous wrote: Hi everyone, I used g_sas: g_sas -s .tpr -f .xtc -n .ndx -o .xvg -or resarea.xvg What I don't understand is why there are 3 columns in the file resarea.xvg although this is what's written in my file: # g_sas is part of G R O M A C S: # # GROtesk MACabre and Sinister # @

Re: [gmx-users] g_hbond

Hi, Let me have a look at the files off-list and I'll probably see what's going on. Erik Carla Jamous skrev 2010-11-04 11.32: Hi Erik, I tried what you said: I made index groups containing only the atoms involved in that hbond and ran g_hbond again. The problem didn't persist. So I wanted

[gmx-users] tip3p itp file parameters

When using the charmm forcefield, the following is the case: 1. ffnonbonded.itp - has listed paramters for tip3p (and other water models) OWT3 and HWT3 2. ffbonded.itp - does not have paramters for OWT3 and HWT3 Does this mean: 1. nonbonded parameters for tip3p are read from ffnonbonded.itp for

Re: [gmx-users] tip3p itp file parameters

Sai Pooja wrote: When using the charmm forcefield, the following is the case: 1. ffnonbonded.itp - has listed paramters for tip3p (and other water models) OWT3 and HWT3 2. ffbonded.itp - does not have paramters for OWT3 and HWT3 Does this mean: 1. nonbonded parameters for tip3p are rea

[gmx-users] box shape

Dear Lina, could you express these commands clearly? I am a new user! editconf -f peptide.pdb/.gro -o peptide_center_in_simulation_ box.gro -center x/2 y/2 z/2 -box x y z genbox -cp peptide_center_in_simulation_box.gro -cs spc216.gro -o they_are_in_the_same_box_now.gro -p topol.top -- gmx-users

[gmx-users] deform option

Hi, I posted this question earlier but no-one answered it to me so I am going to ask this question again. On deform option in .mdp file, what is being done if you are shearing the system? i.e., if I do: deform = 0 0 0 1 0 0 it seems to change box-xy value. but what does it mean? thanks, gc --

Re: [gmx-users] box shape

mustafa bilsel wrote: Dear Lina, could you express these commands clearly? I am a new user! You've been given commands that are almost exactly what you should enter in a terminal. I would suggest you describe exactly why they aren't clear. editconf -f peptide.pdb/.gro -o peptide_center_

Re: [gmx-users] tip3p itp file parameters

Thanks Justin. I was just making sure that I was modifying the relevant files. On Thu, Nov 4, 2010 at 2:17 PM, Justin A. Lemkul wrote: > > > Sai Pooja wrote: > >> When using the charmm forcefield, the following is the case: >> 1. ffnonbonded.itp - has listed paramters for tip3p (and other water

Re: [gmx-users] GB-polarization

Hi! Yes, the GB-polarization energy corresponds to the solvent-solute electrostatics polarization energy. The non-polar part of the solvation energy (the solvent-solvent cavity term and the solute-solvent vdw-term) are named Non. polar solvation (or something like that) in the log-file. /Per

Re: [gmx-users] tip3p itp file parameters

On 5/11/2010 6:36 AM, Sai Pooja wrote: Thanks Justin. I was just making sure that I was modifying the relevant files. You can verify things for yourself by making a .tpr, making the change, making the new .tpr and then using gmxcheck to compare the two. Mark On Thu, Nov 4, 2010 at 2:17 PM,

[gmx-users] Targeted Energy Minimization

Hi Gmxers, Is that possible that in mdp file, only a specifically-targeted part inside/of the protein is energy minimized (EM)? Like, just wanna EM the ligand or one out of the two proteins in protein-docking. Thanks in advance, Yao -- gmx-users mailing listgmx-users@gromacs.org http