Re: [gmx-users] Regarding membrane construction

Dear Venkat, I guess there are some other methods to generate new lipid bilayer construct by using genbox -cp your_membrane_protein -ci lipid_monomer -nmol xxxcalculate by yourself -try 1000 -cs solovents.gro -p top.top -o new_conf.gro or using editconf cat ...Another way, you can try the

[gmx-users] 答复: (no subject)

Thanks a lot for the help. Best regards, Haiping Zhang 发件人: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se 代表 Justin Lemkul jalem...@vt.edu 发送时间: 2014年6月8日 23:39 收件人: gmx-us...@gromacs.org 主题: Re:

Re: [gmx-users] Regarding membrane construction

Thank you Chen for the quick reply. I will try both options. On Mon, Jun 9, 2014 at 12:52 PM, 陈功 gchen...@gmail.com wrote: Dear Venkat, I guess there are some other methods to generate new lipid bilayer construct by using genbox -cp your_membrane_protein -ci lipid_monomer -nmol

Re: [gmx-users] Problem in NVT equilibration

Dear Surinarayanan, You have to create appropriate index file by grouping solvent and solute molecules separately (eg: Protein_ligand_membrane Water_and_ions). On Mon, Jun 9, 2014 at 12:33 PM, Balasubramanian Suriyanarayanan bsns...@gmail.com wrote: Dear User I do a protein ligand

Re: [gmx-users] Some confusion related to extending a simulation

On 6/8/14, 8:05 PM, bharat gupta wrote: Hi, I extended a crashed simulation using the command : mpirun -np 24 mdrun -v -s mdrun.tpr -cpi mdrun.cpt I just stopped the restarted simulation after some time and found that mdrun.log was not updated, because log file and results obtained from

Re: [gmx-users] Problem in NVT equilibration

Sir, Thanks for your reply. I really works. But the next error message was Group SOL_CL not found in indexfile. Maybe you have non-default goups in your .mdp file, while not using the '-n' option of grompp. In that case use the '-n' option But I have really used -n option. regards

Re: [gmx-users] charge groups

Please keep the discussion on the mailing list. On 6/9/14, 3:02 AM, Negar Parvizi wrote: Dear Dr.Lemkul, Thank you very much for your reply. It was very helpful to me. I checked the force field .rtp files. Here I have two questions: 1-Checking the .rtp files of gromos force field, I saw

[gmx-users] NVT equilibration - error message

Thanks for your reply. when I create index file by grouping sol and ions, protein , ligand and lipid it works. But the next error message was Group SOL_CL not found in indexfile. Maybe you have non-default goups in your .mdp file, while not using the '-n' option of grompp. In that case use the

Re: [gmx-users] Regarding membrane construction

On 6/9/14, 3:22 AM, 陈功 wrote: Dear Venkat, I guess there are some other methods to generate new lipid bilayer construct by using genbox -cp your_membrane_protein -ci lipid_monomer -nmol xxxcalculate by yourself -try 1000 -cs solovents.gro -p top.top -o new_conf.gro or using editconf cat

Re: [gmx-users] Problem in NVT equilibration

Hi, No need to group SOL and ions. They will default present in index group as Water_and_ions. Just mention Water_and_ions in your mdp file. On Mon, Jun 9, 2014 at 5:26 PM, Balasubramanian Suriyanarayanan bsns...@gmail.com wrote: Sir, Thanks for your reply. I really works. But the next

Re: [gmx-users] Regarding membrane construction

Thank you Justin. On Mon, Jun 9, 2014 at 5:28 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/9/14, 3:22 AM, 陈功 wrote: Dear Venkat, I guess there are some other methods to generate new lipid bilayer construct by using genbox -cp your_membrane_protein -ci lipid_monomer -nmol xxxcalculate

Re: [gmx-users] Regarding membrane construction

Thanks for correction. i appriciate it :) Chen Gong From: Justin Lemkul Date: 2014-06-09 19:58 To: gmx-users Subject: Re: [gmx-users] Regarding membrane construction On 6/9/14, 3:22 AM, 陈功 wrote: Dear Venkat, I guess there are some other methods to generate new lipid bilayer

Re: [gmx-users] Regarding membrane construction

Dear Justin, I have tried the command genbox -cp protein.gro -cs membrane.gro -o protein_in_membrane.gro but it got hanged. Is there something wrong with the command? On Mon, Jun 9, 2014 at 5:50 PM, 陈功 gchen...@gmail.com wrote: Thanks for correction. i appriciate it :) Chen Gong From:

[gmx-users] g_cluster

Hi List, I have come across mailing list where g_cluster can possibly be used for clustering of docked ligands. I tried g_cluster but it will change the reference coordinates with respect to the receptor. Is there a way to do clustering using g_cluster based on binding site? Many thanks, Neha

[gmx-users] Regarding protein folding kinetics

Dear all I would like to get the protein folding kinetics from the REMD simuliaton I tried using g_kinetics with the fraction of native contact. which says 1 is folded state and 0.6 is partial folded state and 0.2 is unfolded state I am running with the following command but it is not

[gmx-users] Reactive force field

Hello, Could it possible to run the simulation with reactive force field using Gromacs? Nilesh -- 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] Reactive force field

Hello, Could it possible to run the simulation with reactive force field using Gromacs? Nilesh -- 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] specbond identified by pdb2gmx but not added to topology

hi justin gmx-users, meanwhile i had understood that the reference distance in the speconds file is not an upper boundary for possible bonds but the distance itself +/-x. i should have read the manual with more attention before writing to the list. thanks again, vedat dear gmx

Re: [gmx-users] Reactive force field

no. Dr. Vitaly V. Chaban On Mon, Jun 9, 2014 at 3:36 PM, Nilesh Dhumal ndhu...@andrew.cmu.edu wrote: Hello, Could it possible to run the simulation with reactive force field using Gromacs? Nilesh -- Gromacs Users mailing list * Please search the archive at

[gmx-users] g_mmpbsa: MM-PBSA method for GROMACS

Dear GROMACS users, We have developed a new tool, *​​g_mmpbsa* for GROMACS to carry out the MM-PBSA calculations. It uses APBS libraries for the Poisson-Boltzmann calculations. ​ ​Features: - ​​ Include SASA, SAV and WCA ​-like​ non-polar models - It inherits threading (OpenMP)

[gmx-users] helix crossing angle

Dear gromacs users, what tool can I use for calculate the helix crossing angle between two helices? Thanks for your help. -- Natalia Alveal Fuentealba Ingeniera en Bioinformática Laboratory of Membranes Proteins Structure and Signalling Departamento de Fisiología Pontificia Universidad

Re: [gmx-users] g_mmpbsa: MM-PBSA method for GROMACS

On 2014-06-09 21:17, Rashmi wrote: Dear GROMACS users, We have developed a new tool, *​​g_mmpbsa* for GROMACS to carry out the MM-PBSA calculations. It uses APBS libraries for the Poisson-Boltzmann calculations. ​ ​Features: - ​​ Include SASA, SAV and WCA ​-like​ non-polar

Re: [gmx-users] helix crossing angle

On 6/9/14, 3:46 PM, Natalia Alveal F. wrote: Dear gromacs users, what tool can I use for calculate the helix crossing angle between two helices? g_bundle and/or g_helixorient should probably do what you need. -Justin -- == Justin A.

Re: [gmx-users] Regarding membrane construction

On 6/9/14, 9:08 AM, Venkat Reddy wrote: Dear Justin, I have tried the command genbox -cp protein.gro -cs membrane.gro -o protein_in_membrane.gro but it got hanged. Is there something wrong with the command? I wouldn't expect a hang as long as the box is set to appropriate dimensions. The

[gmx-users] -inf potential with TPIC

Hi all, I am having a problem with -inf mu coming out of TPIC calculations. Anyone have some suggestions on how to avoid this? Tabulated potentials? Or can I modify the source code to reject the absurd values that cause this? I read a few old discussions on this, I didnt see much on how to handle

Re: [gmx-users] -inf potential with TPIC

On 6/9/14, 6:41 PM, Rafael I. Silverman y de la Vega wrote: Hi all, I am having a problem with -inf mu coming out of TPIC calculations. Anyone have some suggestions on how to avoid this? Tabulated potentials? Or can I modify the source code to reject the absurd values that cause this? I read a

[gmx-users] charge groups

Dear Dr.Lemkul, Thank you very much for your reply. It was very helpful to me. I checked the force field .rtp files. Here I have two questions: 1-Checking the .rtp files of gromos force field, I saw that always  one hydrogen of NH2 and also the OH group of COOH were not included in the

[gmx-users] (no subject)

Dear users, In a lipid membrane simulation Grompp command gives me a error atom LC# not found. What do I need to change? regards Suriyanarayanan -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! *

Re: [gmx-users] Regarding membrane construction

I have used editconf -f protein.gro -c -bt cubic -d 1.5 -o confout.gro to set the box. Then genbox -cp confout.gro -cs dppc128.gro -o protein_in_membrane.gro got hanged Am I missing something here??? On Tue, Jun 10, 2014 at 2:51 AM, Justin Lemkul jalem...@vt.edu wrote: On 6/9/14, 9:08 AM,

Re: [gmx-users] (no subject)

Hi, Did you modify your forcefield such a way that it applicable for lipid atoms also??? If not, follow Justin's tutorial http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/02_topology.html On Tue, Jun 10, 2014 at 10:31 AM, Balasubramanian Suriyanarayanan