Re: [gmx-users] DSSP

ftp://ftp.cmbi.ru.nl/pub/software/dssp/ There you can find windows .exe version of it. On Tuesday, December 5, 2017, 7:38:44 AM GMT+2, Vidya R wrote: Hi gromacs users, I use gromacs 5.1.4 in *cygwin* (OS windows 7, 64 bit.) I want to download and install

[gmx-users] DSSP

Hi gromacs users, I use gromacs 5.1.4 in *cygwin* (OS windows 7, 64 bit.) I want to download and install dssp tool. How to proceed? Thanks, Vidya.R -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! *

Re: [gmx-users] Conversion of charmm36 parameters from namd to gromacs

On 12/4/17 2:35 PM, Daniel Bauer wrote: Unfortunatly It seems like my university has no contract to access this paper so I cant check the SI. The ones I have are from http://dx.doi.org/10.7554/eLife.25844 (adjusted to better match the free energy of solvation in NMA). There seem to be

Re: [gmx-users] Problem with topology generation by Amber 12 ff

Thanks Dr. Justin, The atoms of Histidine residue formed the dihedral CB, CG, ND1 and CD2. Tracing the residues rtp file in Amber12 ff, I should assign His either HID or HIE, But once I protonate HIS at NE2 only and assign this NE2-protonated HIS as HIE, some of the residues other than this

Re: [gmx-users] request

The error states what the problem is, there are three files that the program expects to be in the directory, but they aren't. Two things can do, change the command line if it is doing not what you want it to (i.e. it is trying to add more data onto an existing simulation, or you have used the

Re: [gmx-users] Conversion of charmm36 parameters from namd to gromacs

Unfortunatly It seems like my university has no contract to access this paper so I cant check the SI. The ones I have are from http://dx.doi.org/10.7554/eLife.25844 (adjusted to better match the free energy of solvation in NMA). On  12/04/2017 07:53 PM, Justin Lemkul wrote: > > > On 12/4/17

Re: [gmx-users] request

What is -s md ? in the command line. On 05-Dec-2017 12:32 AM, wrote: hi.what causes this error? Command line: gmx mdrun -s md -cpi md_0_1_prev.cpt Output file appending has been requested, but some output files listed in the checkpoint file md_0_1_prev.cpt are not

[gmx-users] FaQ paramters for ADP topology with acpype

Dear users, I used acpype to  get a topology for ADP.While minimizing energy one hydrogen moves too much to an oxygen, ending with the oxygen "swallowing" the hydrogen totally. They got exact the same coordinates in the .gro output. In the topology the parameters for that H (h0) are missing: [

[gmx-users] request

hi.what causes this error? Command line: gmx mdrun -s md -cpi md_0_1_prev.cpt Output file appending has been requested, but some output files listed in the checkpoint file md_0_1_prev.cpt are not present or not named as the output files by the current program: Expect output files present:

[gmx-users] request

Command line: gmx mdrun -s md -cpi md_0_1_prev.cpt Output file appending has been requested, but some output files listed in the checkpoint file md_0_1_prev.cpt are not present or not named as the output files by the current program: Expect output files present: Expected output files not

[gmx-users] Same parameters for ADP single P-O bonds and double P=O bonds in in acpype (GAFF) topology

Dear users, I try to simualte PKAC with 1 Mg and ADP (4ntt.pdb).For PKAC and Mg topology I use the GROMACS-2016.3 AMBER99SB-ILDN. For ADP I try to use acpype. The H were assigned with pymol, only getting one at the phosphate groups what should be ok.Nevertheless acpype assigns the same

[gmx-users] request

hi.what causes this error? Command line: gmx mdrun -s md -cpi md_0_1_prev.cpt Output file appending has been requested, but some output files listed in the checkpoint file md_0_1_prev.cpt are not present or not named as the output files by the current program: Expect output files present:

Re: [gmx-users] Conversion of charmm36 parameters from namd to gromacs

On 12/4/17 12:21 PM, Daniel Bauer wrote: Hello, I finally found my error in the conversion. As always, the devil is in the detail. I was under the assumption that parameters listed in the original forcefield files (toppar) are also sigma and epsilon values. However, as you know, the original

[gmx-users] lost particles while sorting

​​Hi, I am running NPT equilibration on gpu. After I finished the NVT I got an error saying Software Inconsistency Error: Lost particles while sorting (6 out of 8) Now I looked into the archive and it seems like a bug which was fixed in gromacs versions > 5.0. I am using gromacs-2016.4 and the

Re: [gmx-users] Conversion of charmm36 parameters from namd to gromacs

Hello, I finally found my error in the conversion. As always, the devil is in the detail. I was under the assumption that parameters listed in the original forcefield files (toppar) are also sigma and epsilon values. However, as you know, the original files list Rmin values (and not sigma). With

[gmx-users] g_sham experimental weighting with temperature

Hi, I hope someone can suggest me any reference or description about the mentioned "experimental energy and temperature weighting" of the tool g_sham. Can I safely use this weighting procedure to obtain reliable PMF plots from a T-REMD simulation? In case of using g_sham with the weighting

Re: [gmx-users] one protein and 4 ligands

On 12/3/17 11:27 PM, Mahboobeh Eslami wrote: Dear justinThank you so muchI did MD simulation on some protein-ligand complexes but I don't know that I must use one mol2 file for 4 ligands or  separate mol2 files for each ligand. I want to calculate free energy value for this complex by

Re: [gmx-users] request

On 12/3/17 11:40 PM, mmahmou...@razi.tums.ac.ir wrote: hi. i have tpr file and cpt file but when i want doing restart for simulation with,gmx mdrun -s file.tpr -cpi file.cpt command I'm having trouble. please guide me With what? You need to be specific about the problem you're having in

Re: [gmx-users] Umbrella sampling simulation stopped in middle.

On 12/4/17 1:33 AM, Sailesh Bataju wrote: Hi, I've started to pull a dimer of isobutane molecules as a production md after npt equilibriation. Here is the md_pull.mdp file for production md. ; Umbrella pulling, production md ; preprocessing parameters title = Umbrella Sampling ; run

Re: [gmx-users] how to creat new.rtp for acetylated lysine (ALY)

On 12/4/17 5:27 AM, Mehreen Jan wrote: HI! Hope you all will be fine. Version : Gromacs5.1.4 Thank you for your reply. According to your advice I have pasted parameters for acetylated lysine (ALY) from “stream/prot/toppar_all36_prot_modify_res.str (RESI ALY)” in the Charmm36ff (merged.rtp).

Re: [gmx-users] Problem with topology generation by Amber 12 ff

On 12/4/17 1:45 AM, Amir Zeb wrote: Hello gmx users, I have generated topology and coordinate files of ZN metalloprotein by Amber 12 ff. Now I am facing this following issue at grompp run: "ERROR 1 [file topol_Protein_chain_A.itp, line 49741]: No default Improper Dih. types" If I use

Re: [gmx-users] Conversion of charmm36 parameters from namd to gromacs

On 12/4/17 7:47 AM, Daniel Bauer wrote: Hello Justin, Thanks for your response. I was under the assumption that entries in [ pairtypes ] are the ones that override standard LJ interactions derived by pairgen. I now know this is a different section. From what you are saying I come to the

Re: [gmx-users] Usage of GROMACS

Hi Momin, Unfortunately, crystalline structures are, as you have experienced, not the easiest thing to simulate using gromac's system building tools. Typically, people working on MOFs, clays, general polymers, and other non-biological systems use something like LAMMPS (or DL_Poly like you have

[gmx-users] Usage of GROMACS

Hello, is GROMACS meant to be used for simulations of crystaline structures (Metal Organic Frameworks, porous materials, minerals, ...)? Almost every paper working on MD simulations with said structures use DL_Poly or other software. So my question would be is there a community that uses

Re: [gmx-users] Conversion of charmm36 parameters from namd to gromacs

Hello Justin, Thanks for your response. I was under the assumption that entries in [ pairtypes ] are the ones that override standard LJ interactions derived by pairgen. I now know this is a different section. From what you are saying I come to the conclusion that the POT O interaction in

Re: [gmx-users] Metal-Protein interactions

Dear Justin I have manually added Cu ion to the protein structure. the total charge of the system is -0.9. How do I make sure that gromacs is considering Cu in +2 state only? thank you On Wed, Nov 29, 2017 at 4:33 PM, RAHUL SURESH wrote: > Thank you Justin. > >

Re: [gmx-users] Topology file of molecule

Dear Justin, Since you last answer, I have been trying to find some description how to perform dihedrals scans using some QM software and Gromacs. I have found out that it used to be some QM software implemented in Gromacs (Orca) but this implementation is not developed anymore and it does not

[gmx-users] how to creat new.rtp for acetylated lysine (ALY)

HI! Hope you all will be fine. Version : Gromacs5.1.4 Thank you for your reply. According to your advice I have pasted parameters for acetylated lysine (ALY) from “stream/prot/toppar_all36_prot_modify_res.str (RESI ALY)” in the Charmm36ff (merged.rtp). As you suggested that just create a new

Re: [gmx-users] force field packages

Hi, Thanks for the tip, I brought the website back up. Most of the relevant force fields are in the repo, however. Mark On Mon, Dec 4, 2017 at 7:54 PM Zahedeh Bashardanesh wrote: > Hi, > > Does anybody know where else to get the reliable amber force field package > for

[gmx-users] force field packages

Hi, Does anybody know where else to get the reliable amber force field package for gromacs except from gromacs website? The webpage has been down since Saturday. Best, --- Zahedeh Bashardanesh, Ph.D. Candidate