[gmx-users] Topology CHarmm

Dear Gromacs users How to execute the file cgenff_charm2gmx.py file? I tried *chmod +x cgenff_charm2gmx.py No result ** python cgenff_charm2gmx.py Usage: DRUG drug.mol2 drug.str charmm36.ff I didnt get any output files -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Structure blowing up after increased the temperature

Thank you for the help Dr. Jsutin On 3/21/17 12:39 PM, Sameer Edirisinghe wrote: > Dear users, > > I'm trying to find the melting point and Tg of my polymer system using > Density vs temperature curve. I'm using all oplsaa forcefield and I'm going > for NVT and followed by NPT equilibration (

Re: [gmx-users] Water molecule starting at atom 39087 can not be settled

On 3/21/17 7:08 PM, liming_52 wrote: The position of the ligand was obtained using autodock vina. The gro file and ITP file were obtained from the PRODRG server (http://davapc1.bioch.dundee.ac.uk/prodrg). Anyway, I added the ions with 0.154 M NaCl. Did these effect my md? PRODRG

Re: [gmx-users] Water molecule starting at atom 39087 can not be settled

The position of the ligand was obtained using autodock vina. The gro file and ITP file were obtained from the PRODRG server (http://davapc1.bioch.dundee.ac.uk/prodrg). Anyway, I added the ions with 0.154 M NaCl. Did these effect my md? -- With my best wishes, Ming Li, PhD Chinese Academy

Re: [gmx-users] Dihedral drivers and 2D Energy Plot in gromacs

On 3/21/17 7:02 PM, Devashish_Das wrote: Thanks for the solution. So, Is it not possible to do 2D-energy plot of AIB-dipeptide with a water box? or only the use of constant box is the problem? You shouldn't be doing the calculations in water at all. From our previous conversation, I

Re: [gmx-users] Dihedral drivers and 2D Energy Plot in gromacs

Thanks for the solution. So, Is it not possible to do 2D-energy plot of AIB-dipeptide with a water box? or only the use of constant box is the problem? On Mon, Mar 20, 2017 at 5:26 PM, Justin Lemkul wrote: > > > On 3/20/17 2:50 AM, Devashish_Das wrote: > >> Thanks for the

Re: [gmx-users] Water molecule starting at atom 39087 can not be settled

On 3/21/17 6:51 PM, liming_52 wrote: Dear Gromacs users,I am trying to run a md using 4n6p.cif obtained from PDB with a ligand. I converted the file into pdb format using DS4.1, and got the file named lactoferrin.pdb. When I directly run the command "gmx mdrun -v -deffnm em", the program

[gmx-users] Water molecule starting at atom 39087 can not be settled

Dear Gromacs users,I am trying to run a md using 4n6p.cif obtained from PDB with a ligand. I converted the file into pdb format using DS4.1, and got the file named lactoferrin.pdb. When I directly run the command "gmx mdrun -v -deffnm em", the program runs and produces the information as

Re: [gmx-users] Structure blowing up after increased the temperature

On 3/21/17 12:39 PM, Sameer Edirisinghe wrote: Dear users, I'm trying to find the melting point and Tg of my polymer system using Density vs temperature curve. I'm using all oplsaa forcefield and I'm going for NVT and followed by NPT equilibration ( Both at 523K) of 400ps each. then after

[gmx-users] NORMAL MODES analysis to compute specific heats

On 3/20/17 9:34 AM, Juan José Galano Frutos wrote: >* Hi there: *>>* I've been googled a bit about this issue ( *>* http://thread.gmane.org/gmane.science.biology.gromacs.user/49139, *>*

[gmx-users] Structure blowing up after increased the temperature

Dear users, I'm trying to find the melting point and Tg of my polymer system using Density vs temperature curve. I'm using all oplsaa forcefield and I'm going for NVT and followed by NPT equilibration ( Both at 523K) of 400ps each. then after the production run (at 523K for 5ns) the system is

[gmx-users] g_mmpbsa

Hi gromacs users, How to install mmpbsa using cgywin? I am using gromacs through cgywin. Thanks, Kulkarni.R -- 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

Re: [gmx-users] pdb2gmx generates very large .top for lipids with charmm36-nov2016.ff

So I found out why I didn't use charmm-gui initially, when using the protein membrane builder it removes the ligand minocycline. I have found a solution, on the unlikely chance what I have done will help someone, I'm going to post what I did. Since I used transformations on the protein (aligning

Re: [gmx-users] DSSP

On 3/21/17 5:13 AM, Aishwarya Dhar wrote: Following procedure I have used 1. Downloaded http://swift.cmbi.ru.nl/gv/dssp/ dssp-2.0.4-linux-i386 and renamed it dssp 2.made dssp executable and moved it to usr/local/bin 3.Then ran the command from the current location where the tpr and trr

Re: [gmx-users] Topology for charmm

On 3/21/17 4:54 AM, RAHUL SURESH wrote: how to generate charmm topology file for gromacs using charmm2gmx python script? I have generated the stream file using cgenff.parachem server.? I wish to have a comprehensive answer Use the CGenFF conversion script here:

Re: [gmx-users] Index is larger than the number of atoms in the trajectory file

On 3/20/17 4:24 PM, Mahboobeh Eslami wrote: Hi all GMX usersI hope you are wellI have simulated a protein-ligand complex. My protein has two calcium ions. I want to use GMXPBSA approach for free energy calculation. If I remove calcium ions, I will get following error in the first step of

Re: [gmx-users] query about structural consistency

I really appreciate your thoughts. I know about the words like "exact" or "correct" does not stand in such scenario. I just needed an expert opinion regarding the quality assurance of the equilibrated structure. People often tend to ask question like how can you say that your model is properly

Re: [gmx-users] NORMAL MODES analysis to compute specific heats

On 3/20/17 9:34 AM, Juan José Galano Frutos wrote: Hi there: I've been googled a bit about this issue ( http://thread.gmane.org/gmane.science.biology.gromacs.user/49139, http://www.gromacs.org/Documentation/How-tos/Normal_Mode_Analysis,

[gmx-users] Fwd: CNT Water and DNA protein, Not working

-- Forwarded message -- From: Abhishek Agrawal Date: Tue, Mar 21, 2017 at 2:25 PM Subject: CNT Water and DNA protein, Not working To: gmx-us...@gromacs.org Hare Krishna Everyone! OBJECITVE: See I am aiming to make a system having CNT Water DNA to study

Re: [gmx-users] query about structural consistency

On Tue, 21 Mar 2017 13:09:46 +0530 abhisek Mondal wrote: > Hi, > > I just have a basic query. > > I'm working with a protein-ligand system with a goal of performing > Umbrella sampling in gromacs. So first, after I build the complex, I'm > going for NVT and

[gmx-users] NORMAL MODES analysis to compute specific heats

Sorry for insisting, but has no-one any idea of this? Thanks Juan José Galano Frutos Department of Biochemistry and Molecular and Cellular Biology, Faculty of Sciences, University of Zaragoza Pedro Cerbuna # 12, 50009 Zaragoza (Spain) +34 976 76 28 06 Institute for Biocomputation and

Re: [gmx-users] query about structural consistency

Hello Mark, I guess that's an endless question and will vary based on what kind of ions used in equilibration. So how do I made a decision that I got the correct equilibrated structure for my production run ? Is it pressure, density, temperature convergence or I'm missing something? On Tue,

[gmx-users] DSSP

Following procedure I have used 1. Downloaded http://swift.cmbi.ru.nl/gv/dssp/ dssp-2.0.4-linux-i386 and renamed it dssp 2.made dssp executable and moved it to usr/local/bin 3.Then ran the command from the current location where the tpr and trr files are present do_dssp -s md.tpr -f md.trr

[gmx-users] Fwd: CNT Water and DNA protein, Not working

-- Forwarded message -- From: Abhishek Agrawal Date: Tue, Mar 21, 2017 at 2:25 PM Subject: CNT Water and DNA protein, Not working To: gmx-us...@gromacs.org Hare Krishna Everyone! OBJECITVE: See I am aiming to make a system having CNT Water DNA to study

Re: [gmx-users] query about structural consistency

Hi, On Tue, Mar 21, 2017 at 8:40 AM abhisek Mondal wrote: > Hi, > > I just have a basic query. > > I'm working with a protein-ligand system with a goal of performing > Umbrella sampling in gromacs. So first, after I build the complex, I'm > going for NVT and

Re: [gmx-users] Regarding extending simulations

Hi, Your first run used gmx mdrun -deffnm, and like the error message says, the checkpoint file knows what the output filenames were in that case. But your second mdrun doesn't specify -deffnm, so mdrun doesn't know whether you meant to append to the old files, or not provide that checkpoint

[gmx-users] Topology for charmm

how to generate charmm topology file for gromacs using charmm2gmx python script? I have generated the stream file using cgenff.parachem server.? I wish to have a comprehensive answer -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] mdp options for REMD

Sure. One takes longer. Mark On Tue, 21 Mar 2017 02:50 YanhuaOuyang <15901283...@163.com> wrote: > Dear Mark, > Do you mean that both "generate at 300K but themostat at > 500K"(gen-temp=300K,ref-t=500K) and "generate at 500K and thermostat at > 500K"(gen-temp=500K, ref-t=500K) are OK?

[gmx-users] query about structural consistency

Hi, I just have a basic query. I'm working with a protein-ligand system with a goal of performing Umbrella sampling in gromacs. So first, after I build the complex, I'm going for NVT and followed by NPT equilibration of 20ns each. After equilibration, is it mandatory that my equilibrated