Re: [gmx-users] (no subject)

Please specify your gromacs version. On Mon, Dec 9, 2019 at 10:04 AM shakuntala dhurua wrote: > hi > I am facing problem during hydrogen bond correlation c(t) with error > segmentation fault > I have used following flag for generate xtc file::- gmx trjconv -n > index.ndx -s ins_prod_1.tpr -f

Re: [gmx-users] CA ions

You are going to the right way. There are more options given in gmx genion. Check -pname and -nname. These options will help you to select the name of positive and negative ions. On Sat, 7 Dec 2019, 5:05 am Iman Katouzian, wrote: > Good day, > > I want to simulate my protein in gromacs and in

Re: [gmx-users] SASA calculation for one replica in REMD

Check gmx sasa -h It is implemented in Gromacs On Tue, Apr 23, 2019 at 2:37 PM Shan Jayasinghe < shanjayasinghe2...@gmail.com> wrote: > Dear Gromacs Users, > > I did replica exchange molecular dynamics simulation which contains 25 > replicas. Now I want to calculate the solvent accessible

Re: [gmx-users] calculating energy between certain groups

First of all define energy groups in mdp file. Then run gmx grompp with that mdp to generate a new tpr. In gmx mdrun provide reference file (eg tpr). On Mon, May 21, 2018 at 7:19 AM, Irem Altan wrote: > I tried the following: > > mdrun -rerun umbrella0.xtc -np cpu -deffnm

Re: [gmx-users] Fwd: how to get .mdp files

mdp file is parameter file for md simulations. You need to copy if you want to use the parameters used in the tutorial. You can also change that parameter according to your use and need. On Sat, Feb 17, 2018 at 7:34 AM, neelam wafa wrote: > -- Forwarded message

Re: [gmx-users] pH dependent simulation

Thanks for correcting.. On Mon, Nov 27, 2017 at 7:02 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 11/27/17 1:02 AM, Tasneem Kausar wrote: > >> pKa of amino acid residue is a constant quantity. Depending on the pH you >> > > That's not strictly true.

Re: [gmx-users] pH dependent simulation

pKa of amino acid residue is a constant quantity. Depending on the pH you can protonate and deprotonate amino acid according to the pKa of particular residue. Virus-free. www.avast.com

Re: [gmx-users] .coordinate(gro) file

Fitsiou already suggested you to change the number of atoms at top second line of the gro file. On Mon, Nov 6, 2017 at 10:22 AM, rose rahmani wrote: > Hi dear > > yes,i did > > On Mon, Nov 6, 2017 at 12:07 AM, Fitsiou, Eleni > > wrote: > > >

Re: [gmx-users] pdb (CTAB) into .GRO

Force field in gromacs reads only standard amino acids/DNA/RNA residue. In your pdb file residue name XXX is not defined in gromos ff. If your system is other than protein then use ATB to generate topolgy.

Re: [gmx-users] itp file for aminoacids

You only need a pdb file for amino acids/proteins. pdb2gmx in gromacs does the job of making itp. Virus-free. www.avast.com

Re: [gmx-users] MD simulation error : rRNA simulaion

In energy group you have given Potein and non-Protein and you are not simulation a protein but RNA. On Fri, Oct 6, 2017 at 12:53 AM, Hemant Arya wrote: > Dear gromacs, > Greetings > I am trying to run a NVT with the following command. > > My mdp file is below > >

Re: [gmx-users] checking simulation progress

see gmx check -h option On 3 Oct 2017 21:33, "Bukunmi Akinwunmi" wrote: > dear gmx-users, > my simulation has been running for sometime but now I want to know how > long is left for the simulation to be completed. I need help with the > command to analyse a running

Re: [gmx-users] autocorrelation function and residence time

r half-life. > > Kind regards, > Erik > __ > Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow > Department of Chemistry – BMC, Uppsala University > +46 (0)18 471 4539 > erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.

Re: [gmx-users] autocorrelation function and residence time

try – BMC, Uppsala University > +46 (0)18 471 4539 > erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se> > > On 21 Sep 2017, at 11:12, Tasneem Kausar <tasneemkausa...@gmail.com< > mailto:tasneemkausa...@gmail.com>> wrote: > > Still waiting for suggest

Re: [gmx-users] autocorrelation function and residence time

Still waiting for suggestions. On Wed, Sep 20, 2017 at 9:42 AM, Tasneem Kausar <tasneemkausa...@gmail.com> wrote: > Dear all > > I want to calculate residence time of interface water molecules at protein > interface. I am using Gromacs-4.6.4. > I am using using following

[gmx-users] autocorrelation function and residence time

time. Thanks in Advance Tasneem Kausar -- 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 http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https

Re: [gmx-users] ERROR IN EXECUTION ---GMX

If you are using linux and gromacs is installed in /user/local/bin check these steps vi ~/.bashrc in the last line of the file add source /usr/local/bin/GMXRC and save this. On Mon, Aug 28, 2017 at 12:08 PM, Neha Gupta wrote: > Hi, > > I gave these commands

Re: [gmx-users] gmx distance

Ctrl+D On Fri, Aug 25, 2017 at 5:06 PM, Sergio Manzetti < sergio.manze...@fjordforsk.no> wrote: > Hello, I am trying to find the average distance between two groups in a > trajectory, defined by the index.ndx file and the traj.xtc, > > the options are > > > Available static index groups: > Group

Re: [gmx-users] problem in extending a simulation run

As error says you have run previous simulation on gromacs-5.0.2 and now you are running with gromacs 5.0.6 On 18 Aug 2017 12:11, "manindersingh rajawat" < rajawat.manindersi...@gmail.com> wrote: > Dear all, > > I want extend a 100ns run to 150 ns. For this I use following commands: > > gmx

Re: [gmx-users] (no subject)

Number of hydrogen bond depends on the nature of your drug. It can be zero, one or many. On Thu, Aug 10, 2017 at 10:33 AM, saranya wrote: > Hi, > I have done protein-drug simulations for 100ns. While calculating the > hydrogen bond between the protein-drug complex I am

Re: [gmx-users] Regarding creating indexing with atoms having same labelling in different molecules

Try this 1 | 13 & a N This will select the group 1 and 13 and all the atom having atom ID N. On Tue, Jul 11, 2017 at 12:19 PM, Dilip H N wrote: > Hello, > I am having problems during creating the indexes for atoms which have same > atom labelling for the two/three

Re: [gmx-users] Fwd: Broken chain / fragmentation

Try -pbc whole On 27 May 2017 18:09, "Biplab Ghosh" wrote: > Dear Gromacs users, > > My Gromacs simulation on a protein terminated without any error and major > warning. However, when I see the conformations, I found them broken. > > For trajectory conversion, I have

Re: [gmx-users] md continuation

You can directly extend time with gmx covert-tpr -s old.tpr -o new.tpr -extend 2 On 18 May 2017 15:34, "Kashif" wrote: > It means I should conver my md.mdp file for 40 ns from 20 ns in the same > folder and then run this command ... > > grompp -f md.mdp -c

Re: [gmx-users] md continuation

see command gmx convert-tpr On Wed, May 17, 2017 at 3:22 PM, Kashif wrote: > I have already run my 20 ns md simulation of my protein. The log file is > showing completion of my 20 ns data. I have also done analysis by using > trjconv command and g_rms. > Now I want

Re: [gmx-users] pdb2gmx handle the dna structure containing potassium

Take a look at you pdb file. May be potassium atom is defined as HETATM in pdb. amber99sb-ildn ff has K in its ions.itp file. On Wed, May 10, 2017 at 1:46 PM, Changdong LIU wrote: > Dear GROMACS users, > > > I used pdb2gmx to generate topology file for the g_quadruplex DNA which >

[gmx-users] Water molecules present at the protein-protein interface.

Dear all I want to figure out dynamics and interaction of water molecules present at the protein-protein interface. My system has around 4 water molecules and 450 amino acid residues. How interface water molecules can be identified from the bulk of water. Thanks in Advance -- Gromacs

[gmx-users] Hydration shell

Dear all Is it possible in gromacs to write trajectory of a system that have interface residues and water molecules of first hydration shell? Thanks in Advance -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before

Re: [gmx-users] Using the md integrator for calculating free energy of solvation

In the last line of mdp file couple-lambda0 and couple-lambda1 have the same vdwq variable. It indicates A and B state of system. So grompp is complaining about the identical states. You can also see the alchemistry.org for detail information about the free energy calculations. On Wed, May 3,

Re: [gmx-users] cant load trajectory, low memory

If you are taking confout.gro as your starting input file, it will have all water and ions of the previous simulation. On Mon, Apr 24, 2017 at 3:35 PM, Tasneem Kausar <tasneemkausa...@gmail.com> wrote: > Create index group that have both protein and ACO. gmx make_ndx will serve &g

Re: [gmx-users] cant load trajectory, low memory

Create index group that have both protein and ACO. gmx make_ndx will serve this task. Then create a pdb file file from gmx trjconv Or you can choose system as output and delete ions and solvent from any editor. On Mon, Apr 24, 2017 at 3:21 PM, abhisek Mondal wrote: >

Re: [gmx-users] powercut command

option. > Only the following extensions are possible: > .trr, .cpt, .tng > > For more information and tips for troubleshooting, please check the GROMACS > website at http://www.gromacs.org/Documentation/Errors > --- >

Re: [gmx-users] powercut command

. This was the reason for error On Thu, Apr 13, 2017 at 3:34 PM, Tasneem Kausar <tasneemkausa...@gmail.com> wrote: > please give the exact command and error message. > > On Thu, Apr 13, 2017 at 3:30 PM, Anshul Lahariya < > anshullahariy...@gmail.com> wrote: > >> dear das

Re: [gmx-users] powercut command

please give the exact command and error message. On Thu, Apr 13, 2017 at 3:30 PM, Anshul Lahariya wrote: > dear das sir, > > -cpi was already added to the command but my problem is not solved > > On Thu, Apr 13, 2017 at 3:24 PM, Anshul Lahariya < >

Re: [gmx-users] COMMAND IN HBOND

If you want to calculate hydrogen bond invloving residue there are two steps >From gmx hbond you can obtain an xpm file where hydrogen bond existance mad is plotted. Then calculate the percentage of hydrogen bond involving residues from script given by justin. -- Gromacs Users mailing list *

Re: [gmx-users] Pull code grompp error

Define you pull group in index file as the error message says. On Fri, Mar 24, 2017 at 12:18 PM, Souparno Adhikary wrote: > Hi, > > Below is my .mdp code for pulling as found in the tutorial by Justin > Lemkul. I made the required changes to match my version syntax. > >

Re: [gmx-users] Error in free energy calculation

If it is so, you may change the position of your drug.itp file in topology > file, means that before the protein topology. > I hope this might solve your problem. > > Good luck! > > Amir > > On Thu, Mar 16, 2017 at 2:49 AM, Tasneem Kausar <tasneemkausa...@gmail.com > >

[gmx-users] Error in free energy calculation

Dear All I am trying to perform free energy calculations of a protein drug system. I am using Gromacs-5.1.4 for this purpose. decoulpe molecule type i.e. drug molecule is defined in separate drug.itp file. From the discussions of mailing list I have found that this is not a problem. To obtain the

Re: [gmx-users] Adding a number of drugs around a polymer

Check gmx insert On 25 Feb 2017 18:12, "faride badalkhani" wrote: > Dear GROMACS users, > > I need to locate a number of drug molecules around one equilibrated polymer > molecule and drugs should be randomly located within a spherical shell from > the polymer surface.

Re: [gmx-users] Extending a program

t; > On Thu, 23 Feb 2017 at 3:21 PM, Tasneem Kausar <tasneemkausa...@gmail.com> > wrote: > > > If you have state.cpt file from the previous simulation, on extending the > > simulation -cpi state.cpt will serve to read the last coordinate of your > > previous s

Re: [gmx-users] Extending a program

If you have state.cpt file from the previous simulation, on extending the simulation -cpi state.cpt will serve to read the last coordinate of your previous simulation. Use this command gmx mdrun -v -deffnm extend.tpr -cpi state.cpt On Thu, Feb 23, 2017 at 12:24 PM, RAHUL SURESH

Re: [gmx-users] deformation in simulation

here is whole command gmx trjconv -f production.xtc -s protein.tpr -o production_pbc.xtc -pbc whole On Thu, Feb 23, 2017 at 3:13 PM, Tasneem Kausar <tasneemkausa...@gmail.com> wrote: > You should apply periodic boundary condition on your protein. > check gmx trjconv -h and selcet

Re: [gmx-users] deformation in simulation

You should apply periodic boundary condition on your protein. check gmx trjconv -h and selcet (-pbc whole) First load protein.gro file in vmd. In vmd main window molecule information is given. Write click on that and then click load data into molecule option. Select protein.xtc file. It will load

Re: [gmx-users] gmx trjcat

See options with gmx trjcat -h On Thu, Feb 23, 2017 at 8:49 AM, YanhuaOuyang <15901283...@163.com> wrote: > Hi, > I have a long trajectory , which is broken into 2 part because of > disk space : traj 1 is 0ns-213ns, the other traj 2 is 200ns-300ns. How to > concatenate this two trajectory

Re: [gmx-users] Hydrogen bond problem

___ > Erik Marklund, PhD > Marie Skłodowska Curie INCA Fellow > Department of Chemistry – BMC > Uppsala Universtity > erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se> > > On 8 Feb 2017, at 06:06, Tasneem Kausar <tasneemkausa...@gmail.com tasneemk

[gmx-users] Hydrogen bond problem

Dear all I am calculating hydrogen bond between protein and drug molecule using gmx hbond tool. I am using default value for hydrogen bond radius. Here is the command: gmx hbond -f protein_drug.xtc -s protein+drug.tpr -hbn hbond.ndx -hbm hbond.ndx I am selecting group 1 and 13. It shows many

Re: [gmx-users] Gro file does not match topology file... continue

You both are right. Previously I was editing the topology file after solvating the protein. So the mismatch error was there. Sorry for the inconvenience... On Sat, Jan 28, 2017 at 7:14 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 1/27/17 8:39 PM, Tasneem Kausar

Re: [gmx-users] Gro file does not match topology file... continue

Yes , you are right. I was also surprised that when atoms in gro and topology match then how this error can be. In my case I was simulating a small peptide segment in water. Everything goes smoothly in it. Then I have generated a system with 8 peptides using genconf command. I have generated a box

Re: [gmx-users] Gro file does not match topology file... continue

I was having the same problem. The atoms in topology and gro were same and this error was there. By increasing box size the problem was resolved. What would be tge reason for that.? On 27 Jan 2017 22:30, "Justin Lemkul" <jalem...@vt.edu> wrote: > > > On 1/27/17 11:48

Re: [gmx-users] Gro file does not match topology file... continue

Increase your box size. On 27 Jan 2017 22:15, "Poncho Arvayo Zatarain" wrote: > > > Hello: according to the queshere abouttion and the answer send me here > about gro (58674) file does not mtch with the topology (58666), i checked > my gro file at the top corner on the

Re: [gmx-users] VMD

May be atom number of your xtc and gro file are not same. Write a new gro file with the same output you are taking for xtc after skiping the frames. On 25 Jan 2017 17:38, "Mark Abraham" wrote: > Hi, > > Indeed. But unless someone knows what you did with trjconv, and

Re: [gmx-users] REGARDING TOPOLOGY FILE

---------- > > > > > > - > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <

Re: [gmx-users] REGARDING TOPOLOGY FILE

ss 12429.154 amu, Density 0.646 g/cc > Added 680 residues. > > Still, there is an error. > > > > > > - > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se>

Re: [gmx-users] REGARDING TOPOLOGY FILE

The error show that the number of atoms in topology file and gro file does not match In last line of topology file define the ligand molecule. here is the exapmle [ molecules ] ; Compound#mols Protein_chain_A 1 DRG 1 On Thu, Jan 19, 2017 at 10:55 AM, Subashini .K

Re: [gmx-users] Topology parameters for ligand

Thank You for your reply The system under my study has positive charge. There are 3 positive charges on the protein and one on drug molecule. How these charges will be handled. On Mon, Jan 9, 2017 at 6:37 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 1/9/17 2:31 AM, tasne

Re: [gmx-users] Topology parameters for ligand

ing the state B of the ligand in topology, how the ligand molecule will be decoulped in complex. On Sun, Jan 8, 2017 at 10:21 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 1/7/17 10:29 PM, tasneem kausar wrote: > >> Thank you for your reply >> >> In

Re: [gmx-users] Topology parameters for ligand

ot; <jalem...@vt.edu> wrote: > > > On 1/7/17 6:05 AM, tasneem kausar wrote: > >> Dear all >> >> I am following Justin's tutorial methane in water for free energy >> calculation. I am using Gromacs-5.1.4. The charges of methane in topology >> are s

[gmx-users] Topology parameters for ligand

Dear all I am following Justin's tutorial methane in water for free energy calculation. I am using Gromacs-5.1.4. The charges of methane in topology are set to zero. So following the same protocol, is it relevant to set the charges at zero in topology of the drug. I am confused because in

Re: [gmx-users] Free energy calculation of protein and drug

rational to simulate the system with one ff and then > change the ff for free energy calculations > > good luck > > On Jan 7, 2017 2:01 PM, "tasneem kausar" <tasneemkausa...@gmail.com> > wrote: > > > Thanks Amir Zeb for your reply > > I have read in lite

Re: [gmx-users] Free energy calculation of protein and drug

in gromos54a7 format. Since I didn't find free energy calculation of protein and ligand with this force field. Thats why I was confused to proceed further using the same. On Sat, Jan 7, 2017 at 10:07 AM, tasneem kausar <tasneemkausa...@gmail.com> wrote: > mm/pbsa calculates binding energy. I

Re: [gmx-users] Free energy calculation of protein and drug

mm/pbsa calculates binding energy. I have used that. On Sat, Jan 7, 2017 at 10:00 AM, Amir Zeb <zebami...@gmail.com> wrote: > hello > you may use mm/pbsa compiled with gromacs to calculate free energy > all the best > > On Jan 7, 2017 1:27 PM, "tasneem kausar" <

[gmx-users] Free energy calculation of protein and drug

Dear gromacs users It is first time I am trying to perform free energy calculation of protein and drug complex. I am following Justin' s tutorial of mehtane in water. That calculation are performed on a neutral system. If the ligand molecule has charge what are the provisions that could be taken

[gmx-users] Free energy calculation of protein and drug

Dear all It is first time I am calculating free energy of protein and ligand. I am following the Justin's tutorial of methane in water free energy calculations. Though only van der waal lambda are defined so I have taken the mdp files from the alchemistry.org web page. Since the ligand and

[gmx-users] Free energy calculation of protein and ligand

Dear all It is first time I am calculating free energy of protein and ligand. I am following the Justin's tutorial of methane in water free energy calculations. Though only van der waal lambda are defined so I have taken the mdp files from the alchemistry.org web page. Since the ligand and

[gmx-users] Free energy calculation of protein and ligand

Dear all It is first time I am calculating free energy of protein and ligand. I am following the Justin's tutorial of methane in water free energy calculations. Though only van der waal lambda are defined so I have taken the mdp files from the alchemistry.org web page. Since the ligand and

[gmx-users] Free energy calculation of protein and ligand

Dear all It is first time I am calculating free energy of protein and ligand. I am following the Justin's tutorial of methane in water free energy calculations. Though only van der waal lambda are defined so I have taken the mdp files from the alchemistry.org web page. Since the ligand and

Re: [gmx-users] DMSO

Check the total number of atoms in DMSO molecule. after grompp you got an error of non-matching atom in gro and top file. Subtract the number of molecule of top file from molecule of gro file. Divide the subtracted number with coordinates of DMSO. This gives the number of DMSO molecule. Add this

Re: [gmx-users] Charge on drug

Thank you I have generated the itp file from ATB. It works fine. On Wed, Dec 21, 2016 at 7:48 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 12/19/16 1:23 PM, tasneem kausar wrote: > >> Thank you for reply >> What type of refinements are needed in t

Re: [gmx-users] Charge on drug

in advance On 19 Dec 2016 18:31, "Justin Lemkul" <jalem...@vt.edu> wrote: > > > > On 12/19/16 5:31 AM, tasneem kausar wrote: >> >> Thanks for reply >> >> I have visualized solvate.gro and em.gro. Some bonds that are not present >>

Re: [gmx-users] Charge on drug

solvate.gro is box.gro file. It was typing mistake. On Mon, Dec 19, 2016 at 4:01 PM, tasneem kausar <tasneemkausa...@gmail.com> wrote: > Thanks for reply > > I have visualized solvate.gro and em.gro. Some bonds that are not present > in box.gro is seen in em.gro. > I a

Re: [gmx-users] Charge on drug

isualization_Software# > Topology_bonds_vs_Rendered_bonds > for what's probably going on. > > Mark > > On Mon, 19 Dec 2016 19:05 tasneem kausar <tasneemkausa...@gmail.com> > wrote: > > > Dear All > > > > > > I am using Acpype server to generate topology f

[gmx-users] Charge on drug

Dear All I am using Acpype server to generate topology file of drug molecule to perform protein drug MD simulation. Acpype have generated the itp file and other necessary for MD simulations. I am doing MD on gromacs 5.1.4 software using amber99sb force field. When I have done energy minimization

[gmx-users] Charge Correction using HF method

Dear Justin Sir I am doing protein and drug MD simulation. I have generated the itp file of drug from PRODRG. I have calculated the charge on the atom using HF/6- 31G* basis set from orca3.0. Is this a right protocol to use it in GROMACS for the charge correction. With Regards Tasneem --

[gmx-users] Problem in mdrun

= 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp= 300.0 gen_seed= 173529 Kindly tell me where I am missing. Thanks in advance. With Regards Tasneem Kausar -- Gromacs Users mailing list * Please search the archive at http

Re: [gmx-users] (no subject)

Dear Kingsley You are directly calculating the rms after combining the xtc file. It is clear from the warning that you did not apply perodic boundary condition on you trajectory. Try trjconv -f combined.xtc -s refrence.tpr -o combined_pbc.xtc -pbc whole -center command after trjcat. After

Re: [gmx-users] MD simulations of two chains protein

I have suggested you in previous mail to plot chain A and chain B separately. I have looked at the link. It is because of the same residue number in chain A and chain B. In xvg file chain identifier (A/B) will not be shown. Just open .xvg file in any text editor. Copy the residue number and their

Re: [gmx-users] MD simulations of two chains protein

Plot chain A and chain B separately. Residue no. in both the chain are started from 1. It will overlap in same plot. On Mon, Nov 14, 2016 at 5:03 PM, Khadija Amine wrote: > Dear Gromacs users, > > I need your help regarding MD simulation of two chains protein. > The chain A

Re: [gmx-users] trr file

Hi I think you can try analysis in more than one step by using -b and -e option of trjconv. On Fri, Oct 14, 2016 at 5:59 PM, Mark Abraham wrote: > Hi, > > Prevention is the best medicine - ask google about reducing GROMACS > trajectory storage volume :-) > > Mark > >

Re: [gmx-users] Protein Drug simulation Parameters

influence on binding energy. On Tue, Sep 27, 2016 at 5:16 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 9/27/16 7:32 AM, tasneem kausar wrote: > >> Thank you Justin for your reply. >> There is another question regarding MMPBSA energy calculations. I have &

Re: [gmx-users] Protein Drug simulation Parameters

conditions like whole and nojump effect the binding energy. On Mon, Sep 26, 2016 at 5:41 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 9/26/16 4:43 AM, tasneem kausar wrote: > >> Dear All >> >> I have performed MD simulation of protein and drug crystal structure

[gmx-users] Protein Drug simulation Parameters

Dear All I have performed MD simulation of protein and drug crystal structure. I have generated drug itp file from PRODRG server and corrected the charges of atoms as suggested in Justin's paper J. Chem. Inf. Model. 2010, 50, 2221–2235. I have done 50 ns MD simulation of protein and drug using

[gmx-users] Error in installing Gromacs in Cygwin

Dear all I have installed gromacs-5.1.2 in cygwin 64 bit computer. cmake have finished successfully during installation. While executing the command "cygcheck /usr/local/gromacs/bin/pdb2gmx.exe" it gives following error- cygcheck: track_down: could not find cyggmx-6.dll cygcheck: track_down:

[gmx-users] problem in editing .eps file of hbond

Dear all I have plotted the hydrogen bonds present at the interface of protein in its binary complex. I have already written the index file for the interface residues then used it for hydrogen bond calculation. There are a number of bonds at the interface. I am trying to put a cut off of 50 % for

[gmx-users] g_mmpbsa positive binding energy

Dear Gromacs Users I am trying to calculate binding energy of protein-ligand and protein-receptor complex using g_mmpbsa. I have run simulation of 10 ns and snapshot was generated at every 1 ps. Initial 2ns was not taken. g_mmpbsa was run for the rest of the frames. The command line was given as:

[gmx-users] vacuum simulation vs specific solvent simulation

Dear users Dear gromacs users As Joao replied and asked about the purpose of simulation. I have performed the vacuum simulation. I want to see the secondary structure change in vacuum and in specific solvent. mdp parameters are :. ; ;User spoel (236) ;Wed Nov 3 17:12:44 1993 ;

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 137, Issue 14

gt; > You can reach the person managing the list at > gromacs.org_gmx-users-ow...@maillist.sys.kth.se > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gromacs.org_gmx-users digest..." > > > Today's Topics: >

[gmx-users] vacuum simulations

Dear gromacs users I have performed the vacuum simulation of protein. The structure was minimized after generating the box using the following mdp parameters. ; ;User spoel (236) ;Wed Nov 3 17:12:44 1993 ;Input file ; cpp = /usr/bin/cpp define =

[gmx-users] vaccume simulation

Dear gmx-users I am trying to calculate rmsd for protein backbone. I have done simulation in vacuum. There are for negative charges in the system. During solvation via genbox, 4 water molecule were added using -maxsol. The charges have been neutralized by addition of 4 Na ion and water molecules

[gmx-users] forming disulfide linkage between two chains

sir I am trying to make disulfide linkage between chain A and B. The command line is pdb2gmx -f prtn.pdb -o prtn.gro -p prtn.top -ss. I have used -ss option of pdb2gmx but disufide linkage is not formed between the chains A and B. What is the possible way to form the disulfide linkage in Gromacs

[gmx-users] g_anaeig error

for PCA i used the g_covar followed by g_anaeig. for g_anaeig i am using the eigenvec.trr file and averagr.pdb file these files are generated by g_covar. g_anaeig gives the following message; There were 40 inconsistent shifts. Check your topology where is the problem occured? -- Gromacs Users

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 131, Issue 49

of an ion from alchemical transformation (Wojciech Kope?) 2. umbrella sampling tutorial (Ming Tang) 3. Re: enemat output (Mark Abraham) 4. g_anaeig error (tasneem kausar) 5. Thermostats and MSD (sujithkakkat .) 6. Re: g_anaeig error (Tsjerk Wassenaar) 7. Compiler