Re: [gmx-users] Values for pcon & ncon in G_mmpbsa

Post this on g_mmpbsa forum https://groups.google.com/forum/#!forum/g_mmpbsa Regards Sarath On 5 July 2016 at 08:57, Amali Guruge wrote: > Dear All, > > In my MD simulation I only added counter ions (20 Na+ ions) to neutralize > the system. Now I want to do MM_PBSA calculations for my MD runs.

Re: [gmx-users] do_dssp version error

dssp by default gets installed as mkdssp. Do an export DSSP=path_to_mkdssp_executable and it will worl On 12 September 2016 at 18:01, Samith Rathnayake wrote: > Dear all > > When i'm run the do_dssp command in the gromacs > > do_dssp -f ../run01/run01.trr -s ../run01/run01.tpr -sc scount.xvg -

Re: [gmx-users] RMSD of interested region?

Create two index groups. One with 28-197 residues and second group with 2-27. Supply this index file to gmx rms (if using 5.1) with -n option and select 28-197 as fit group and 2-27 for RMSD analysis. Regards, Sarath On 20 September 2016 at 12:05, Seera Suryanarayana wrote: > Dear gromcas use

[gmx-users] Porting to Gromacs of Parmbsc1

I wish to use Parmbsc1 for DNA simulations. Are there any timelines to port Parmbsc1 into Gromacs along with amber14sb? Regards, Sarath -- 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 h

Re: [gmx-users] Porting to Gromacs of Parmbsc1

o multiple people, and a validation > script can show it works correctly with respect to the reference > implementation, then we'll consider it for inclusion in GROMACS. > > Mark > > On Sun, 14 Feb 2016 14:39 Sarath Chandra > wrote: > > > I wish to use Parmbsc1 fo

Re: [gmx-users] umbrella simulation PMF curve

Your umbrellas are not well spaced. There is a gap at 1.2, 2.25 and around 4.4 which is affecting your pmf profile. Add more simulations at those points and re-check again. Regards, Sarath On 22 February 2016 at 11:09, Nikhil Maroli wrote: > Hello , > > can anyone tell me why im getting profi

Re: [gmx-users] Problem in implementing do_dssp

do_dssp is looking for /usr/local/bin/dssp and if your dssp executable has some other name do_dssp will fail. Before you run do_dssp you need to set the DSSP variable. for bash environment do this: export DSSP=`which dssp-2.0.4-linux-amd64` Regards, Sarath -- Sarath Chandra Dantu, PhD, ELS

Re: [gmx-users] Problem in implementing do_dssp

dssp executable generally gets installed as mkdssp. Check if this is the case. Regards, Sarath -- Sarath Chandra Dantu, PhD, ELS Room No. 606, New BSBE Building Department of Biosciences and Bioengineering Indian Institute of Technology Bombay Powai Mumbai, 400-076, India On 6 April 2016 at

Re: [gmx-users] LINCS error in MD simulation

parameters, and the mdp settings will present you with the solution of this problem. Regards, Sarath -- Sarath Chandra Dantu, PhD, ELS Room No. 606, New BSBE Building Department of Biosciences and Bioengineering Indian Institute of Technology Bombay Powai Mumbai, 400-076, India On 11 April 2016 at

Re: [gmx-users] RMSD calculation of protein-ligand complex

You can make an index group with both protein+ligand using make_ndx command and use the index file from make_ndx to run the rmsd analysis Regards, Sarath -- Sarath Chandra Dantu, PhD, ELS Room No. 606, New BSBE Building Department of Biosciences and Bioengineering Indian Institute of

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 144, Issue 140

Add the following line to your .bashrc or .cshrc source /usr/local/gromacs/bin/GMXRC and then everytime you open a new terminal gromacs will be auto sourced. Regards, Sarath -- Sarath Chandra Dantu, PhD, ELS Room No. 606, New BSBE Building Department of Biosciences and Bioengineering Indian

Re: [gmx-users] Syntax error

You have to provide the actual box vectors value in numbers eg: -box 9 5 6 regards, Sarath -- Sarath Chandra Dantu, PhD, ELS Room No. 606, New BSBE Building Department of Biosciences and Bioengineering Indian Institute of Technology Bombay Powai Mumbai, 400-076, India On 26 April 2016 at 13

Re: [gmx-users] Compiling g_correlation

You have to use gromacs 3.3 and also will need lamboot and other dependencies. Let me know how you progress. I recently installed it On Apr 27, 2016 8:35 PM, "Jorge Fernández de Cossío Díaz" < j.cossio.d...@gmail.com> wrote: > I'm trying to use g_correlation ( > http://www.mpibpc.mpg.de/grubmuelle

Re: [gmx-users] Cyclic peptide - topology reconstruction

-- Sarath Chandra Dantu, PhD, ELS Room No. 606, New BSBE Building Department of Biosciences and Bioengineering Indian Institute of Technology Bombay Powai Mumbai, 400-076, India On 29 April 2016 at 16:50, Ferdous, Saba wrote: > Dear Gromacs Support, > > I am writing regarding cyclic

Re: [gmx-users] on HS14 atomtype

What command did you use (pdb2gmx/grompp)? You have to check whether your ligand.itp is referenced in your topol.top for grompp to find the atomtypes present in your gro. Regards, Sarath -- Sarath Chandra Dantu, PhD, ELS Room No. 606, New BSBE Building Department of Biosciences and

Re: [gmx-users] on HS14 atomtype

tt > > > > > > > > > > At 2016-05-12 15:03:59, "Sarath Chandra" > wrote: > >What command did you use (pdb2gmx/grompp)? You have to check whether your > >ligand.itp is referenced in your topol.top for grompp to find the > atomtypes > >pr

Re: [gmx-users] Help required for calculation of protein coverage % wrt time

Regards, Sarath -- Sarath Chandra Dantu, PhD, ELS Room No. 606, New BSBE Building Department of Biosciences and Bioengineering Indian Institute of Technology Bombay Powai Mumbai, 400-076, India On 19 May 2016 at 18:35, Antara mazumdar wrote: > Dear gromacs users, > > I have a p

Re: [gmx-users] help required in calculating npme value for domain decomposition

Please refer to documentation on tune_pme in version 5.1.2 or g_tune_pme in older versions of gromacs. Regards, Sarath On 19 May 2016 at 23:43, Antara mazumdar wrote: > Dear gromacs users, > > I need help in calculating the value of npme for the purpose of domain > decomposition for my syst

Re: [gmx-users] (no subject)

, Sarath -- Sarath Chandra Dantu, PhD, ELS Room No. 606, New BSBE Building Department of Biosciences and Bioengineering Indian Institute of Technology Bombay Powai Mumbai, 400-076, India On 14 June 2016 at 15:13, Sepideh Momeninezhad < sepideh.momeninez...@gmail.com> wrote: > dear grom

Re: [gmx-users] Problem in rmsf calculation

If you have selected C-alpha atoms on x-axis rmsf tool will write C-alpha atom index number so that is why you do not see 1-143. Run a gawk on your RMSF output to set the column 1 right. On 16 June 2016 at 10:48, Seera Suryanarayana wrote: > Dear gromacs users, > > After mdrun I have plotted

Re: [gmx-users] MD Analysis

You have to frame a more specific question and then check the manual about the list of tools gromacs has to offer. Accordingly you can use the appropriate tool which suits your needs. Internet has the following tutorial to offer: http://www.drugdesign.gr/uploads/7/6/0/2/7602318/lecture_mdanalysis.

Re: [gmx-users] TRR file in VMD

Did you run trjconv? Might be a pbc issue. And also work with xtc , less bulky On Jun 28, 2016 10:29 AM, wrote: > Hello users, > When I am loading data (.trr) into my structure file (.gro) in VMD. The > trajectories are showing some kind of grid. It's like VMD is showing the > path of a traje

[gmx-users] dielectric constant effect on protein, dna, water interface

Fellow users, I am working on a Protein-DNA complex and I have a question regarding the electrostatic interaction energies calculated at the interface of protein, DNA and water. I am using amber99sb+parambsc0 forcefield for my system with TIP3P water simulated using gromacs4.6.4. I understand th