[gmx-users] Do I need to repeat my MD simulation ?

Dear all, I did a MD simulation (GROMACS 4.5 G53a6 force field) on protein-peptide complex for 5ns and got an interesting conformational change of T-loop. However, when I rerun my script using the same input file in the same machine, I can not observe the same or similar conformational

Re: [gmx-users] distance between protein and ligand

Hi, Did u repeat your MD simulation of your docked complex ? I also asked the similar question. Alex replied : I would start several (5-10?) runs with different (random) starting impulse to get more reliable data. Best Shiyong On Tue, Oct 9, 2012 at 12:48 PM, Archana Sonawani

Re: [gmx-users] Interaction study for peptide-receptor..

Hi, Your expectation from MD is too much than reality. Peptide design is an open problem. Lots of elegant protocols are available. However, to my understanding, the core problem is still about protein-peptide docking and scoring. MD simulation only helps on some special cases. It is impossible

Re: [gmx-users] Interaction study for peptide-receptor..

Justin, Single mutation for four residue. The number of mutants is 4x19=76 Of course , that is a tiny peptide library. Best Shiyong On Wed, Oct 10, 2012 at 9:06 AM, Justin Lemkul jalem...@vt.edu wrote: On 10/9/12 8:43 PM, Liu Shiyong wrote: Hi, Your expectation from MD is too much

[gmx-users] PRODRG tools

Dear all, Is there any other free tool like PRODRG ? PRODRG server couldn't read PDB file from user any more. It 's not easy to get a free version asap. Best Shiyong -- Shiyong Liu -- Biomolecular Physics and Modeling

[gmx-users] trjconv with superposition

Dear Colleagues, I want to extract PDB snapshot from trajectory file by following command. It works in 4.0, but not in 4.5 pdb=1akk trjconv -f ${pdb}_gromos53a6_MD2.traj.trr -o ${pdb}_gromos53a6_MD2.traj.xtc trjconv -s ${pdb}_gromos53a6_MD2.tpr -f ${pdb}_gromos53a6_MD2.traj.xtc -dt 20 -b 0 -o

Re: [gmx-users] Which FF could be used for protein-RNA MD simulation in GROMACS?

GROMACS - Have a Nice Day On Fri, Dec 10, 2010 at 11:57 AM, Justin A. Lemkul jalem...@vt.edu wrote: Liu Shiyong wrote: Hi,  I just tried G53a6 for protein-RNA simulation. But fatal error shows up. That's a useless description of the problem.  Exact input and output would be necessary

Re: [gmx-users] Which FF could be used for protein-RNA MD simulation in GROMACS?

: [DEPRECATED] Gromacs force field (see manual) 36: [DEPRECATED] Gromacs force field with hydrogens for NMR On Sat, Dec 11, 2010 at 4:05 PM, Liu Shiyong liushiy...@gmail.com wrote: I compiled the new version GROMACS 4.5.3 and installed according to http://www.gromacs.org/Downloads

Re: [gmx-users] Which FF could be used for protein-RNA MD simulation in GROMACS?

I tried amber99 and amber03. I got the same error info : Opening force field file /usr/local/share/gromacs/top/amber03.ff/aminoacids.hdb Opening force field file /usr/local/share/gromacs/top/amber03.ff/dna.hdb Opening force field file /usr/local/share/gromacs/top/amber03.ff/rna.hdb Opening force

[gmx-users] Which FF could be used for protein-RNA MD simulation in GROMACS?

Hi, I just tried G53a6 for protein-RNA simulation. But fatal error shows up. Opening library file /usr/share/gromacs/top//FF.dat Select the Force Field: 0: GROMOS96 43a1 force field 1: GROMOS96 43a2 force field (improved alkane dihedrals) 2: GROMOS96 45a3 force field (Schuler JCC 2001 22

Re: [gmx-users] Which FF could be used for protein-RNA MD simulation in GROMACS?

Thanks. I will upgrade to Version 4.5 and use AMBER. I like G53a6, but it surprised me without RNA parameter. On Fri, Dec 10, 2010 at 11:57 AM, Justin A. Lemkul jalem...@vt.edu wrote: Liu Shiyong wrote: Hi,  I just tried G53a6 for protein-RNA simulation. But fatal error shows up

[gmx-users] gromacs

Dear all, I download gromacs-4.0.5 and installed it. I got the test by git. git clone git://git.gromacs.org/regressiontests.git then: Testing fe_test . . . PASSED Testing field . . . FAILED. Check checkvir.out (264 errors) files in field Testing nacl . . . PASSED Testing sw . . . PASSED

[gmx-users] Re: gromacs

=spc 12-34.5967-42.0952 0.0977748 1aml.pdb with G53a6 using vsite=none and water=spce There were 2/45 differences in final energy with the reference file pdb2gmx tests FAILED On Wed, Apr 21, 2010 at 4:36 PM, Liu Shiyong liushiy...@gmail.com wrote: Dear all, I download gromacs-4.0.5

Re: [gmx-users] energy groups

energy groups --- On Fri, Jan 30, 2009 at 5:11 PM, Justin A. Lemkul jalem...@vt.edu wrote: Liu Shiyong wrote: --- Program grompp, VERSION 4.0.2 Source code file: grompp.c, line: 150

Re: [gmx-users] energy groups

: Alright, so how about the other comment I made? Are you using the right coordinate file? I recall you got this error when you used the non-pdb2gmx processed .pdb file as input into grompp. You must use the coordinate file that corresponds to your topology. -Justin Liu Shiyong wrote

Re: [gmx-users] energy groups

On Mon, Feb 2, 2009 at 5:26 PM, Justin A. Lemkul jalem...@vt.edu wrote: Liu Shiyong wrote: pdb2gmx -ignh -ff G53a6 -f r-l_365130_G53a6.minim_traj_withH.pdb -p r-l_365130_G53a6.minim_traj_withH_0.6.top -i r-l_365130_G53a6.minim_traj_withH_0.6.posre.itp -o r-l_365130_G53a6

Re: [gmx-users] energy groups

74 75 76 77 2569 2570 [ chC__!H* ] 2571 2575 2576 2577 2578 2580 2581 2582 2583 2584 2585 2586 2587 2588 2589 2590 2591 2592 2593 2594 2595 2597 2598 2599 2600 2601 2602 2605 2606 2607 On Mon, Feb 2, 2009 at 5:46 PM, Justin A. Lemkul jalem...@vt.edu wrote: Liu Shiyong

Re: [gmx-users] energy groups

error: atoms 1 and 2 in charge group 1 of molecule type 'Protein_A' are in different energy groups --- It's Against the Rules (Pulp Fiction) On Mon, Feb 2, 2009 at 7:05 PM, Mark Abraham mark.abra...@anu.edu.au wrote: Liu Shiyong wrote: command

[gmx-users] energy groups

Hi, I tried to make energy groups based on chain id and atom type. My purpose is to select atoms in chain A and B without Hydrogen atoms . This is the command: make_ndx -f a.pdb -o a.ndx make_ndx.input a.log cat make_ndx.input del 1-9 chain A and B !a H* chain C !a H* q And then run

Re: Fwd: [gmx-users] Invalid atom number 6415 in indexfile

Hi, On Wed, Jan 28, 2009 at 6:31 PM, Mark Abraham mark.abra...@anu.edu.auwrote: Liu Shiyong wrote: Hi, *Step 2:* Starting structure: clean2.pdb I am trying to calculate the energy according to energy groups pdb2gmx -ff G53a6 -f clean2.pdb -p clean2_0.6.top -i clean2_0.6

Re: Fwd: [gmx-users] Invalid atom number 6415 in indexfile

On Wed, Jan 28, 2009 at 6:32 PM, Justin A. Lemkul jalem...@vt.edu wrote: Liu Shiyong wrote: Hi, Thank for your helpful reply. I understand your feeling. If you have time, please see the following. mdrun has an option to output the final structure(-c). I just knew it after reading

Re: Fwd: [gmx-users] Invalid atom number 6415 in indexfile

an option to output the minimized structure. Thanks to all. On Thu, Jan 29, 2009 at 12:26 PM, Justin A. Lemkul jalem...@vt.edu wrote: Liu Shiyong wrote: *.gro has no chain id information. I can not make energy group(based on chain id) from *.gro file generated by pdb2gmx See the mail I

Re: [gmx-users] Invalid atom number 6415 in indexfile

Hi, Did you get my script ? I dump a frame from .trr file. I did not define xtc-grps On Wed, Jan 21, 2009 at 2:00 PM, Justin A. Lemkul jalem...@vt.edu wrote: Liu Shiyong wrote: Hi, I got an error when do grompp: The input PDB file comes from the output of GROMACS by trajconv command

[gmx-users] charge groups

Hi, In the manual: Consider a water molecule interacting with another atom. When we would apply the cutoff an on atom-atom basis we might include the atom-Oxygen interaction(with a charge of -0.82) without the compensating charge of the protons and so induce a large dipole moment over

Fwd: [gmx-users] Invalid atom number 6415 in indexfile

, to just run the commands interactively until you have everything flowing. -Justin I dump a frame from .trr file. I did not define xtc-grps On Wed, Jan 21, 2009 at 2:00 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: Liu Shiyong wrote: Hi, I got

[gmx-users] Invalid atom number 6415 in indexfile

Hi, I got an error when do grompp: The input PDB file comes from the output of GROMACS by trajconv command. *Here is the log from grompp:* Option Filename Type Description -f em.mdp Input, Opt! grompp input

Re: [gmx-users] Qestion about how to define groups by chain id in a protein ?

see, atoms 1996 and 1998 should be in different groups. I have no any idea whether it's related to Gromacs or to the pdb file, or to something else? Could anybody advice SOMETHING? On Mon, Jan 19, 2009 at 11:59 AM, Justin A. Lemkul jalem...@vt.edu wrote: Liu Shiyong wrote: Hi, I searched

Re: [gmx-users] Qestion about how to define groups by chain id in a protein ?

Thanks. I used the PDB file with H . It works though it's still a mystery for me why PDB file without H couldn't work. On Tue, Jan 20, 2009 at 1:53 PM, Justin A. Lemkul jalem...@vt.edu wrote: Liu Shiyong wrote: snip The problem lies here: Including chain 1 in system: 1296 atoms 125

[gmx-users] Is there any option to output interaction energy based on energy groups?

Hi, Is there any option to output total interaction energy (without *internal energy*) based on energy groups? *g_energy -f r-l_365130_G53a6.minim_traj_withH_0.6.minim_ener.edr* [shiy...@reco temp20090115]$ g_energy -f r-l_365130_G53a6.minim_traj_withH_0.6.minim_ener.edr

Re: [gmx-users] Qestion about how to define groups by chain id in a protein ?

2024 2025 2026 2027 1996 and 1998 are in different energy groups. What is the meaning of the charge group 296 of molecule type 'Protein_B' ? On Fri, Jan 16, 2009 at 9:19 PM, Mark Abraham mark.abra...@anu.edu.auwrote: Liu Shiyong wrote: Hi, We have a protein with two chains A and B

[gmx-users] Qestion about how to define groups by chain id in a protein ?

Hi, We have a protein with two chains A and B. We want to calculate the interaction energy only. Would you advise how to define the energy groups for the chains and how to output the interaction energy between chains A and B ? -- Shiyong Liu Postdoc center for bioinformatics in the university

[gmx-users] trjconv chaged the chain names of multi-chain complex?

Hi, Chain name is very important for some application. But, when I use the following script to get a minimized structure from a multi-chain complex. But the chain name was changed. I checked the man trjconv , but I did not find any information on chain name for trjconv. pdb2gmx -ff

[gmx-users] amber force field problem: ignh doesnot work

Hi, I install amber force filed according to source: http://chemistry.csulb.edu/ffamber/index.html But , I run pdb2gmx, I got a problem. Program pdb2gmx, VERSION 3.3.1 pdb2gmx -ignh -ff amber99 -f r-l_1.pdb Opening library file /export/apps/gromacs-3.3.1-Amber

[gmx-users] How to change the default value for pbc ?

Hi, I generated mdout.mdp by grompp -f em.mdp -c ${file}_box.gro -p ${file}.top -o ${file}.input.tpr . The pbc in mdout.mdp is like: ; Periodic boundary conditions: xyz (default), no (vacuum) ; or full (infinite systems only) pbc = xyz It seems that grompp doesnot give

Re: [gmx-users] How to change the default value for pbc ?

specified, with all the defaults. Add the pbc=whatever line into your INPUT mdp to fix this. - Original Message From: Liu Shiyong [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Thursday, March 13, 2008 11:39:46 PM Subject: [gmx-users] How to change

[gmx-users] converged to Epot

Hi, Now, I do minimization. It's converged to Fmax 100. How can I change it into Epot ? For example, Epot(n)-Epot(n-1) / Epot(n-1) 5% n is the step. Step= 1891, Dmax= 1.2e-03 nm, Epot= -4.08327e+04 Fmax= 1.31834e+03, atom= 6946 Step= 1892, Dmax= 1.5e-03 nm, Epot= -4.08334e+04 Fmax=

[gmx-users] trjconv output at a specified time

Hi, I want to output a structure in a given time, for example , in step 1 during minimization. I tried the following command using dump: trjconv -f r-l_1_oplsaa.minim_traj.trr -timestep 1 -o m.pdb -s r-l_1_oplsaa.input.tpr -t0 0 -dump 1 But It didnot work. Output msg: Select a group: 2

Re: [gmx-users] trjconv output at a specified time

On Wed, Mar 12, 2008 at 5:32 PM, Alan Dodd [EMAIL PROTECTED] wrote: You asked for the frame at 1ps. The trajectory starts at 125ps, so unsurprisingly the program does not give you an output. - Original Message From: Liu Shiyong [EMAIL PROTECTED] To: Discussion list for GROMACS

[gmx-users] parameter on Energy Minimization

Hi, I used a script given below for energy minimization of a native protein-protein complex 1akj. I removed HETATMs and water molecules from the structure, and the minimized structure (1akj_oplsaa.minim_traj.pdb) with epsilon_r=80. Then I used rasmol to check the result. The ligand is ran

Re: [gmx-users] parameter on Energy Minimization

Thanks Mark and Justin. I did experiment with the following editconf.It works. Thanks. editconf -f ${file}.gro -o ${file}_box.gro -d 0.75 -bt cubic By the way, how to select box size automatically ? I just gave an arbitrary number: 0.75 Another question is how to get the

Re: [gmx-users] minimized on protein-protein decoys

Hi, Mark, Thanks for reply. On Sun, Mar 9, 2008 at 1:41 AM, Mark Abraham [EMAIL PROTECTED] wrote: Liu Shiyong wrote: Hi, all My purpose is to get the binding energy by gromacs. You can't do this without water. The binding energy involves displacing water interactions. Yes

[gmx-users] minimized on protein-protein decoys

Hi, all My purpose is to get the binding energy by gromacs. I tried to minimize protein-protein docking decoy by using gromacs without water. But after being minimized, the ligand ran away from receptor. That's not what I expected . I just want to relax the protein-protein interface due to some