Re: [gmx-users] Simulation with ligand on protein surface

Hi Justin and sorry for the vagueness What I'm observing are displacements from the binding site (granted, they are quite shallow) and loss of any relation to the experimental data. They also happen fairly fast (often below 10ns) and just looking at the trajectory, makes me think something is

[gmx-users] RB dihedral type in amber99sb-ildn ffbonded.itp

Dear All, I need to impose a distance restraints between COM of protein active site residues and COM of a ligand. But the problem is I am using an .itp file generated from acpype. While I use the ligand.itp externally, I can not impose the distance restraints between the protein and the ligand. Th

Re: [gmx-users] Adding missing heavy atoms

Hi Prasun, If you really want to prepare the structure of a molecule, better try any modelling software. GaussView could be a handy option. Export your molecule in .pdb format and a little bit of modification will make your nucleotide ready to use. Best wishes, Tarak On Sat, Jul 11, 2015 at 10:33

[gmx-users] Adding missing heavy atoms

Dear All I have generated the base atoms of nucleotides in a structure, but it does not have sugar and phosphate atoms. Is there any method by which I can add them appropriately (either in A or B form) Thanx in advance PRASUN (ASHOKA) Desire + stability = Resolution Resolution + Hard work = Succes

Re: [gmx-users] (no subject)

Hi PAULAMI, Use gmx trjcat to concatenate the two trajectory files and then calculate the rmsd. http://manual.gromacs.org/programs/gmx-trjcat.html Best wishes, Tarak On Thu, Jul 9, 2015 at 1:34 PM, PAULAMI CHATTERJEE < chatterjee_paul...@yahoo.co.in> wrote: > Dear All, > I have a 30 ns trajecto

Re: [gmx-users] Dihedral copying from itp to ff

Dear Justin and Mark, I also need to impose a distance restraints between COM of protein active site residues and COM of a ligand. But the problem is I am using an .itp file generated from acpype. While I use it externally I can not impose the distance restraints between the protein and the ligand

Re: [gmx-users] Question regarding box size

Thanks Justin and Victor On Sat, Jul 11, 2015 at 9:12 AM, Justin Lemkul wrote: > > > On 7/10/15 1:35 AM, James Lord wrote: > >> Hi all, >> I have a system with 300k atoms, but computationally it is expensive for >> me >> doing simulation with such a big system, Is it possible to reduce the box >

Re: [gmx-users] How to justify when the trajectory reached equilibrium

I see. Thanks. Qing At 2015-07-11 05:07:27, "Justin Lemkul" wrote: > > >On 7/9/15 11:00 PM, Qing Lv wrote: >>> It means to evaluate quantities over successive blocks of time (e.g. using >>> -b and -e that all GROMACS analysis tools support) and check to see whether >>> or not the quantities

[gmx-users] difference between steep and cg

Dear Gromacs experts, I am quite confused about the difference between the energy minimization algorithm steep and cg. According to my experience, MPI is not suitable for cg. Sometimes, even if the system has already converged using steep algorithm, it can be further minimized if one changes th

Re: [gmx-users] restrain COM of a group of atoms

Dear Chaban, Thanks for your explanation, and sorry for the late reply. I didn't notice the error when doing mdrun. For one pull-coordn-groups, we need to define two groups. So my aforementioned code is not correct. But I still did not find out a way feasible to restrain the COM of the referen

Re: [gmx-users] trouble diagnosing a simulation that's blowing up (shake not converging --> segmentation fault)

Hi, Sorry, I mean your [molecules] section. The order there, and the atom orders looked up from [moleculetypes] imply the required atom ordering for a matching .gro. Run grompp and see what it says. Mark On Sat, Jul 11, 2015 at 3:27 AM Nathan K Houtz wrote: > Hi, > > Thanks Mark. I'm sorry tho

Re: [gmx-users] trouble diagnosing a simulation that's blowing up (shake not converging --> segmentation fault)

Hi, Thanks Mark. I'm sorry though, I don't think I understand what you mean. I thought the [system] section of the topology file was just a name for the system. How should I imply an order for the atoms? I did double check that the ordering in atoms is the same as it is in my .gro file (grommp

Re: [gmx-users] trouble diagnosing a simulation that's blowing up (shake not converging --> segmentation fault)

Hi, That could only happen if your grompp -c input used a different atom ordering from that implied by your [system] section of your .top. grompp warns about this, but maybe you didn't notice... (Or the structure you loaded into VMD is a mismatch to the trajectory, so its heuristics for guessing w

Re: [gmx-users] trouble diagnosing a simulation that's blowing up (shake not converging --> segmentation fault)

Actually, I think I found the problem. When i looked at the pdb files in vmd the first time I missed it, but a colleague had a hunch and I found that he was right! I think that shake is constraining atoms to the wrong molecules. Here's a screenshot I took where you can see what I mean:http://img

Re: [gmx-users] Question regarding box size

On 7/10/15 1:35 AM, James Lord wrote: Hi all, I have a system with 300k atoms, but computationally it is expensive for me doing simulation with such a big system, Is it possible to reduce the box size? If yes how? (the .gro file is uploaded). I know from Justin tutorial genconf -nboxvec

Re: [gmx-users] Problem with the MDS extended trajectory in Gromacs 5.04

On 7/10/15 6:39 AM, PAULAMI CHATTERJEE wrote: Thank you Justin for the suggestion. I was able to obtain a full trajectory using trjcat. However I would also like to mention that the exact commands I have shown in my previous mails produced the files with 'the names'. Can you please tell me

Re: [gmx-users] Grompp Error No default Ryckaert-Bell. types

On 7/10/15 9:47 AM, Anurag Dobhal wrote: Dear gromacs users. I am simulating a molecule in opls-aa force field. While running energy minimization I did get the error "No default Ryckaert-Bell. types". I checked the line in topol.top and it says that dihedral for ( C-CT-OH-HO) has No default R

Re: [gmx-users] Simulation with ligand on protein surface

On 7/10/15 5:02 AM, az wrote: Hi all I was wondering if anyone had experience/pointers regarding simulating protein-ligand systems where the interface was heavily surface-exposed ? I've been running quite a few of those these days with Amber99SB--ildn, TIP3P, and acpype (i.e. Ambertools) for l

Re: [gmx-users] How to justify when the trajectory reached equilibrium

On 7/9/15 11:00 PM, Qing Lv wrote: It means to evaluate quantities over successive blocks of time (e.g. using -b and -e that all GROMACS analysis tools support) and check to see whether or not the quantities of interest are varying over time or if they are stable, i.e. converged. Thank yo

Re: [gmx-users] trouble diagnosing a simulation that's blowing up (shake not converging --> segmentation fault)

On 7/9/15 9:23 PM, Nathan K Houtz wrote: Thanks for your explanations, Dr. Lemkul. I had already corrected a couple of the things you suggested. Gromacs won't actually let me run with Nose-Hoover and Parrinello-Rahman together (or at least, it gives a warning not to do that and stops). I'd l

Re: [gmx-users] Free energy change with harmonic restraints

Dear Asaf, I hope you have had a great weekend! I have tried applying TI with restraint-lambdas to measure the free energy difference of applying restraints without success (no dhdl files were being outputted). The tutorial in the link provided by Hannes Loeffler I have looked over before, but

Re: [gmx-users] Question regarding box size

You can reduce the box size with editconf. If you start with a protein, you can add a layer of water of a given thickness by using genbox. Hope this helps Victor 2015-07-10 0:35 GMT-05:00 James Lord : > Hi all, > I have a system with 300k atoms, but computationally it is expensive for me > doi

Re: [gmx-users] g_hbond

I don't understand why am I not getting hydrogen bond,if I use cufoff 0.25nm? Nilesh > But without contact you will need a full donor-hydrogen-acceptor triad for > it to be registered, which is not what you want as far as I can tell. > > Erik > >> On 10 Jul 2015, at 15:17, Nilesh Dhumal wrote: >

Re: [gmx-users] g_hbond

But without contact you will need a full donor-hydrogen-acceptor triad for it to be registered, which is not what you want as far as I can tell. Erik > On 10 Jul 2015, at 15:17, Nilesh Dhumal wrote: > > This is index file > > [ O8-H18-1 ] > 8 18 > [ O8-H18-2 ] > 4032 > > > Found 1 donors

Re: [gmx-users] g_hbond

This is index file [ O8-H18-1 ] 8 18 [ O8-H18-2 ] 4032 Found 1 donors and 2 acceptors Its look contact YES check the distance between accetpr---donor. I will run without contact. Nilesh > Hi Nilesh, > > Am not sure it accepts hydrogens as donors/acceptors even with -contact. > How many d

Re: [gmx-users] g_hbond

Hi Nilesh, Am not sure it accepts hydrogens as donors/acceptors even with -contact. How many donors and acceptors are found? Kind regards, Erik > On 10 Jul 2015, at 14:37, Nilesh Dhumal wrote: > > I calculated number of hydrogen bond with cutoff 0.25 nm (Distance between > hydrogen and O,acce

[gmx-users] Grompp Error No default Ryckaert-Bell. types

Dear gromacs users. I am simulating a molecule in opls-aa force field. While running energy minimization I did get the error "No default Ryckaert-Bell. types". I checked the line in topol.top and it says that dihedral for ( C-CT-OH-HO) has No default Ryckaert-Bell. types. but on checking ffbond

Re: [gmx-users] g_hbond

I calculated number of hydrogen bond with cutoff 0.25 nm (Distance between hydrogen and O,acceptor) using g_hbond, g_hbond -f test.pdb -s 3.tpr -n hydrogen_1.ndx -num test_num.xvg -nonitacc -r 0.25 -contact -dist The found the calculated number of hydrogen bond along time are zero and -nan is the

Re: [gmx-users] Problem with the MDS extended trajectory in Gromacs 5.04

Thank you Justin for the suggestion. I was able to obtain a full trajectory using trjcat. However I would also like to mention that the exact commands I have shown in my previous mails produced the files with 'the names'. Can you please tell me if I want to have the full trajectory from the e

Re: [gmx-users] gmx 5.0 installation with cuda

On Fri, Jul 10, 2015 at 07:10:46PM +0900, Raju wrote: > Dear all, > > > I have installed cuda driver 7.0 in centos6.6 version has default gcc 4.4.7. > > > After the successful installation of cuda, i tried to install gmx 5.0.5 and > found that gmx 5.0.5 version needs over gcc 4.6. > Therefore

Re: [gmx-users] How to mention torsional parameter in toplogy

Hi Mark, Thanks for you valuable advice. Your advice about tabulated entry was very helpful. As you said I read chapter 4 and 5 of manual. Since the equation used in the paper doesn't match any of the standard type mentioned in the manual, I have to use tabulated entry. I have 2 question in this re

[gmx-users] gmx 5.0 installation with cuda

Dear all, I have installed cuda driver 7.0 in centos6.6 version has default gcc 4.4.7. After the successful installation of cuda, i tried to install gmx 5.0.5 and found that gmx 5.0.5 version needs over gcc 4.6. Therefore, i updated gcc 4.4 to 4.7 through devtoolset. When i try to install th

Re: [gmx-users] Free energy change with harmonic restraints

I think It means that, you can use "restraint-lambdas" as a vector to control the restraints (bond, angle dihedral) while using the pull-code and get the corresponding free energy change (I suppose). -- Thanks and Regards, Bipin Singh On Fri, Jul 10, 2015 at 12:39 AM

[gmx-users] Simulation with ligand on protein surface

Hi all I was wondering if anyone had experience/pointers regarding simulating protein-ligand systems where the interface was heavily surface-exposed ? I've been running quite a few of those these days with Amber99SB--ildn, TIP3P, and acpype (i.e. Ambertools) for ligand parametrization, mainly