[gmx-users] question

Dear Justin I was really confused. I know that my peroblem is in incorrect entries (LYS2 and GLU2) in aminoacids.rtp file Sinse I want to have a isopeptide bond between (CD atom of GLU residue from chain B and NZ atom of LYS residue from chain E), thus I should use one HZ atom (for LYS2) and one

[gmx-users] water box moves during MD simulation

Dear all, After MD dynamic simulation for 100 ps, I found the water box was moving during the simulation, but my protein was inside the water box all the time. Here is the . mdp file I used: integrator = md dt = 0.001 nsteps = 10 nstxout = 1000

Re: [gmx-users] water box moves during MD simulation

Hi, You can add (say) -1.23 to every x coordinate and you have a description of the same system. So you can pick any of these for doing the simulation, and any of these for representing the trajectory afterwards. Mark On Wed, May 20, 2015 at 11:19 AM Ming Tang m21.t...@qut.edu.au wrote: Dear

Re: [gmx-users] question

On 5/20/15 3:21 AM, Andrew Bostick wrote: Dear Justin I was really confused. I know that my peroblem is in incorrect entries (LYS2 and GLU2) in aminoacids.rtp file Sinse I want to have a isopeptide bond between (CD atom of GLU residue from chain B and NZ atom of LYS residue from chain E),

Re: [gmx-users] Lincs all-bonds causing instability in otherwise stable system

Hi, Sorry that was so painful for you. The LINCS documentation in the manual suggests that that combination of bonds becoming constraints won't work well. Perhaps we should add a 3-edge cycle detector to grompp? If you actually want a rigid planar DMSO, then three real atoms and a virtual site

Re: [gmx-users] SOL LJ and Coul energies

Hi, On Wed, May 20, 2015 at 6:08 AM Quentin Kaas q.k...@imb.uq.edu.au wrote: Dear all, I am trying to compute the interaction energy between a small peptide and water from a short MD simulation (54a7, reaction-field, Verlet, GPU, gmx 5.04, 1 peptide, 3200 SOL molecules). I have specified

Re: [gmx-users] water box moves during MD simulation

Dear Brother， What does Mark mean？ Sent from my Huawei Mobile Mark Abraham mark.j.abra...@gmail.com wrote: Hi, Nothing wrong with the .mdp file. But you should check your assumption that there's a single meaningful location where an infinite periodic system should be located :-) There's lots

Re: [gmx-users] water box moves during MD simulation

Hi, Nothing wrong with the .mdp file. But you should check your assumption that there's a single meaningful location where an infinite periodic system should be located :-) There's lots of equivalent representations, so mdrun suits itself. Mark On Wed, May 20, 2015 at 9:05 AM Ming Tang

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 133, Issue 107

Thanks Justin for your reply Below is the file where I added h1 parameters in gbsa.itp...In the same way I added the parameters for all the possible atomtypes from gaff ff [ implicit_genborn_params ] ; atype sar st pi gbr hct ;Br 0.1 1 1

[gmx-users] Generate the water box

Dear Gromacs Users, Can I generate only water on the Gromacs? I need water box only. Thank you Tuong Vy -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

[gmx-users] pdb2gmx: intra-chain disulfide bond missing problem

Dear GROMACS users, Can I ask a disulfide bond question if possible? The link below is my protein L50K.pdb with 5 disulfide bonds. https://copy.com/kPLlSianI4LtohNy After using gmx pdb2gmx -f L50K.pdb -o L50K_processed.gro -water spce -inter -ignh -merge interactive one of the disulfide

Re: [gmx-users] Protein-Ligand complex Implicit simulation

Please remember to use a proper subject line and don't reply to the whole digest. On 5/20/15 9:54 AM, sunita gupta wrote: Thanks Justin for your reply Below is the file where I added h1 parameters in gbsa.itp...In the same way I added the parameters for all the possible atomtypes from gaff

Re: [gmx-users] Generate the water box

On 5/20/15 11:55 AM, 姚懿 wrote: genbox without adding a protein. More specifically (and for 5.0): gmx solvate -cs water.gro -box (whatever size is needed) -Justin On Wed, May 20, 2015 at 9:56 AM, Vy Phan phanvy120...@gmail.com wrote: Dear Gromacs Users, Can I generate only water on

Re: [gmx-users] pdb2gmx: intra-chain disulfide bond missing problem

On 5/20/15 12:17 PM, Zhang, Cheng wrote: Dear GROMACS users, Can I ask a disulfide bond question if possible? The link below is my protein L50K.pdb with 5 disulfide bonds. https://copy.com/kPLlSianI4LtohNy After using gmx pdb2gmx -f L50K.pdb -o L50K_processed.gro -water spce -inter

Re: [gmx-users] Generate the water box

genbox without adding a protein. On Wed, May 20, 2015 at 9:56 AM, Vy Phan phanvy120...@gmail.com wrote: Dear Gromacs Users, Can I generate only water on the Gromacs? I need water box only. Thank you Tuong Vy -- Gromacs Users mailing list * Please search the archive at

[gmx-users] Editconf error

Dear GMX users. Im trying to create my system and When i use pdb2gmx everything seems ok. gmx pdb2gmx -f trim.pdb -o trim.gro -water spce -chainsep id Including chain 1 in system: 3235 atoms 203 residues Including chain 2 in system: 2531 atoms 161 residues Including chain 3 in system: 2546

Re: [gmx-users] Editconf error

On 5/20/15 5:27 PM, Jorge Dagnino wrote: Dear GMX users. Im trying to create my system and When i use pdb2gmx everything seems ok. gmx pdb2gmx -f trim.pdb -o trim.gro -water spce -chainsep id Including chain 1 in system: 3235 atoms 203 residues Including chain 2 in system: 2531 atoms 161