[gmx-users] Ligand in PRODRG server is protonated. Why?

Dear gromacs users, I am doing MD simulation of protein-ligand complex. For ligand, I used PRODRG server. My ligand is Tamoxifen (C26H29NO = 57 atoms). I have 3D structure of Tamoxifen from PDB ID 1YA4 (name of Tamoxifen in this pdb file is CTX). In PRODRG outputs, ligand is protonated on N atom

[gmx-users] charge correction in prodrg

Dear Justin, Thanks for your answer. Does ATB need no correction? Best, Andrew -- 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)su

[gmx-users] charge correction in prodrg

Dear gromacs users, I want to do MD simulation of some protein-ligand complexes. For ligand molecules, I used prodrg server. How to do charge correction in prodrg results. Please guide me about that. Best, Andrew -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.o

[gmx-users] part of ligand molecule leaves protein

Hi gromacs users, I did md simulation of the protein-ligand complex. As shown in figure, after 50 ns, part of ligand molecule leaves protein. I remind that I resolve pbc problem at first. https://1drv.ms/u/s!AveJH4Y30cH0tFp_XYCqkrCd7Kqq What is the reason of this state? Best, Andrew -- Gromac

[gmx-users] interrupt of gmx mdrun

Hi gromacs users, I am doing MD simulation of a protein (from pdb ). After equilibration phases, I used following commands: gmx_mpi grompp -f md.mdp -c npt.gro -t npt.cpt p topol.top -o md.tpr -n index.ndx gmx_mpi mdrun -v -nb gpu -deffnm md >& md.job & But, mdrun was interrupted in step 82375

[gmx-users] hydrophobic interactions

Dear Sudip, Thanks for answer. gmx sasa gives data such as area vs time, area vs residue and area vs atom. But I want to have the number of hydrophobic interaction between protein and ligand during the trajectory and get those residues took part in this type of interactions. Best, Andrew -- Grom

[gmx-users] hydrophobic interactions

Hi all, I did md simulation of protein-ligand complex using gromacs 5.1.3. 1) How to investigate hydrophobic interactions between protein and ligand during trajectory? Which tool is appropriate for this aim? 2) How to get an average structure from whole of trajectory? Best, Andrew -- Gromacs U

[gmx-users] trjconv (File input/output error)

Dear gromacs users For fixing PBC problem, I used following command: gmx_mpi trjconv -f md.trr -s md.tpr -n index.ndx -o new.xtc -pbc nojump But I encountered with: Program gmx trjconv, VERSION 5.1.3 Source code file: /root/gromacs_source/gromacs-5.1.3/src/gromacs/utility/futil.cpp, line: 469

[gmx-users] question

Dear Mark and Alex, I want to use CNTs as drug carrier. I think I should consider water molecules inside the CNT. Do I think right? Best, AB -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? R

[gmx-users] gmx distance

Hi, I want to calculate distance between com of 2 groups (3 and 8) gmx_mpi distance -f md.xtc -s md.tpr -n index.ndx -oav dist.xvg After that: Available static index groups: Group 0 "System" (27599 atoms) Group 1 "Other" (716 atoms) Group 2 "MMM" (704 atoms) Group 3 "LIG" (12 atoms) Gr

[gmx-users] question

Hi, I want to do md simulation of adsorbsion on small molecule on cnt and encapsulation small molecule into cnt. Should I remove water molecules inside of cnt? Do these molecules interfere with the interaction between cnt and small molecule? Thanks AB -- Gromacs Users mailing list * Please sea

[gmx-users] Can not write a pdb file without atom names (concatenating 2 pdb files)

Dear Mark, Thanks for your reply. > PDB format needs atom names but trjcat only knows how to read those > from a -s input file. There is no -s option (for tpr file) in the trjcat command. gmx_mpi trjcat -f 9_ms.pdb 19.pdb -o mix.pdb -settime -s md.tpr Error in user input: Invalid command-lin

[gmx-users] Can not write a pdb file without atom names (concatenating 2 pdb files)

Dear gromacs users, I have 2 trajectory files as pdb format. I want to have only one file using the following command: gmx_mpi trjcat -f 9_ms.pdb 19.pdb -o mix.pdb -settime I encountered with: - Command line: gmx_mpi trjcat

[gmx-users] Can not write a pdb file without atom names (concatenating 2 pdb files)

Dear gromacs users, I have 2 trajectory files as pdb format. I want to have only one file using the following command: gmx_mpi trjcat -f 9_ms.pdb 19.pdb -o mix.pdb -settime I encountered with: --- Command line: gmx_

[gmx-users] Gromacs installation on GPU

Dear Gromacs users, I had installed gromacs using following commands: tar xvf cmake-3.6.1.tar.gz tar xvzf gromacs-5.1.3.tar.gz cd ../cmake-3.6.1. ./configure make make install cd ../gromacs-5.1.3 mkdir build cd build cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_MPI=ON -DG

[gmx-users] running MD on gpu (Fatal error)

Dear Gromacs users, I am running MD on gpu using following command line: gmx_mpi mdrun -nb gpu -v -deffnm gpu_md But, I encountered with: GROMACS version:VERSION 5.1.3 Precision: single Memory model: 64 bit MPI library:MPI OpenMP support: enabled (GMX_OPENMP_MAX_T

[gmx-users] Failed to execute command: Try specifying your dssp version with the -ver option.

Also, I have located dssp program in /usr/local/bin -- 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:

[gmx-users] Failed to execute command: Try specifying your dssp version with the -ver option.

Dear Gromacs users, I did MD simulation of my peptide on Gromacs 5.1.3. I want to do do_dssp analysis. After using following command: gmx_mpi do_dssp -f *.xtc -s *.tpr -n index.ndx -o -sc Fatal error: Failed to execute command: Try specifying your dssp version with the -ver option. According t

[gmx-users] bash: /home/linux/installation/gromacs/bin/gmx_mpi: cannot execute binary file

Dear gromacs users, export SOFT=$HOME/installation export CPPFLAGS="-I$SOFT/include" export LDFLAGS="-L$SOFT/lib" export PATH="$PATH":$SOFT/bin tar xvf cmake-3.6.1.tar.gz cd ../cmake-3.6.1. ./configure --prefix=$SOFT make make install tar xvzf gromacs-5.1.3.tar.gz cd ../gromacs-5.1.3 mkdir

[gmx-users] bash: /home/linux/installation/gromacs/bin/gmx_mpi: cannot execute binary file

Dear gromacs users, export SOFT=$HOME/installation export CPPFLAGS="-I$SOFT/include" export LDFLAGS="-L$SOFT/lib" export PATH="$PATH":$SOFT/bin tar xvf cmake-3.6.1.tar.gz cd ../cmake-3.6.1. ./configure --prefix=$SOFT make make install tar xvzf gromacs-5.1.3.tar.gz cd ../gromacs-5.1.3 mk

[gmx-users] viscosity and surface tension

Dear gromacs users, How to calculate viscosity and surface tension in the simulation of some small molecules in the box of water. Best, Andrew -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post?

[gmx-users] question

Dear Justin, My previous problem was solved after I used all-bonds instead of hbonds in constraint section of mdp file. (I got the topology for my ligand using antechamber). After completion of NVT equilibration phase, I viewed nvt.gro using vmd. Please see the related figure in the following li

[gmx-users] question

Dear Justin, Thanks for your quick answer. I want to know about 704, 705 in following line: Double sids (704, 705) for atom 2525 Double sids (704, 705) for atom 2526 Double sids (704, 705) for atom 2527 Double sids (704, 705) for atom 2528 Double sids (704, 705) for atom 2529 Double sids (704,

[gmx-users] question

I obtained my lig.gro using editconf and lig.itp using antechamber. I added lig.gro to conf.gro (for RNA). I included lig.itp to topolo.top file. Double sids (704, 705) for atom 2525 Double sids (704, 705) for atom 2526 Double sids (704, 705) for atom 2527 Double sids (704, 705) for atom 2528 D

[gmx-users] question

Dear gromacs users I am doing md simulation of rna-ligand system using gromacs 5.0.5. In equilibration phase (NVT), I encountered with following error? GROMACS: gmx mdrun, VERSION 5.0.5 Executable: /share/apps/gromacs/bin/gmx Library dir: /share/apps/gromacs/share/gromacs/top Command lin

[gmx-users] amber99bsc0 force field

Dear all Is there amber99bsc0 in gromacs default force fields? Best, Andrew -- 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)subsc

[gmx-users] K+ ions instead of NA+ for neutralization

Dear gromacs users, For neutralizing the simulation system, can I use K+ ions instead of NA+? Best, Andrew -- 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

[gmx-users] (no subject)

Dear Mark and Justin I read Atila question in mailing list. If I use ATB (http://compbio.biosci.uq.edu.au/atb/) for ligand topology preparation, should I modify and correct the charges like the PRODRG server? Best, Andrew -- Gromacs Users mailing list * Please search the archive at http://w

[gmx-users] question

Dear Gromacs users, I am beginner in gromacs. I have a question. Can I do MD simulation of a proccess such as protein aggregation (not folding), fibrillogenesis and fibril formation of proteins? Is this possibility for such aims using Gromacs package? Any help will highly appreciated. -- Groma

[gmx-users] edr file

Dear Justin, Thanks for your answer. I know, Energy minimization causes energy to go down. For example, in following lines, I want to know what value is for step 12 or step 22 in energy minimization? > 11.00 -91587.226562 > 13.00 -93838.976562 or > 21.00 -99023.46093

[gmx-users] edr file

Dear gromacs users After energy minimization, I used g_energy to obtain potential energy vs em steps. g_energy -f em.edr -o potential.xvg. In potential.xvg, some lines are not seen: 0.00 -61742.609375 1.00 -65717.562500 2.00 -75257.804688 3.00 -83263.312500

[gmx-users] question

Dear Justin I was really confused. I know that my peroblem is in incorrect entries (LYS2 and GLU2) in aminoacids.rtp file Sinse I want to have a isopeptide bond between (CD atom of GLU residue from chain B and NZ atom of LYS residue from chain E), thus I should use one HZ atom (for LYS2) and one

[gmx-users] question

Dear Justin Based on your answer (You don't want to be adding 2 HZ here, just one since it is a peptide bond.), I modified LYS2 in aminoacids.hdb file LYS2 2 1 1 H N -C CA 1 4 HZ NZ CE CD But, after pdb2gmx, I encountered with WARNING: atom HZ1 is missing in residue LYS 540 in the pdb file

[gmx-users] question

Dear Tsjerk, Justin and Mark Very thanks for your answers and guidance. I installed gromacs 5.0.5. I used gmx pdb2gmx -f be_near.pdb -ignh -merge all. I want to have a link between two chains (CD atom of GLU residue from chaim B and NZ atom of LYS residue from chain E) to get isopeptide bond bet

[gmx-users] question

Dear Mark I installed the newest version of cmake (3.2.2). After using cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON CUDA_TOOLKIT_ROOT_DIR not found or specified -- Could NOT find CUDA (missing: CUDA_TOOLKIT_ROOT_DIR CUDA_NVCC_EXECUTABLE CUDA_INCLUDE_DIRS CUDA_CUDART_LIBRARY) (R

[gmx-users] question

Dear Justin Thanks for your answer. At first, I installed cmake 2.8.8 on centOS, by following commands: ./bootstrap; gmake; make install Then I used *Quick and dirty *installation instruction. When

[gmx-users] question

Dear Tsjerk I used pdb2gmx -f be_near.pdb -ignh -merge Thanks in advance. -- 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)subscri

[gmx-users] question

Dear Tsjerk residue numbers in chain B are as 220-434. GLU residue is 380. residue numbers in chain E are as 435-551. LYS residue is 540. How to merge these two chains through these two residues? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Maili

[gmx-users] question

Dear Tsjerk Thanks for your quick answer. Yes, I want to have a link between two chains (GLU from chain B and LYS from chain E). I am using gromacs 4.5.3. Can I use the option -merge in this version? After using -merge with pdb2gmx, I encountered with: Invalid command line argument: -merge How

[gmx-users] question

After using pdb2gmx, my terminal output is as follows: Using the Gromos43a1 force field in directory gromos43a1.ff Opening force field file /usr/local/gromacs/share/gromacs/top/gromos43a1.ff/watermodels.dat Select the Water Model: 1: SPCsimple point charge, recommended 2: SPC/E extended s

[gmx-users] question

Dear Justin In pdb file, I corrected the distance between the two residues I want bonded together to form the isopeptide bond (within 10% of my criterion (0.13 nm). The new distance is 0.128 nm. I used following specbond.dat, residuetyps.dat and aminoacids.rtp files.

[gmx-users] question

Dear Justin, For 2 new entries in aminoacids.rtp file, I deleted OE2 atom of GLU residue and HZ2 and HZ3 atoms of LYS residue. Is it true? I compared CYS and CYS2 residues in aminoacids.rtp file, in both case all atoms exist (unlike my case). But there are difference in charges and charge groups.

[gmx-users] question

Dear Justin Thanks for your attention. I viewed coordination file, distance between these atoms are greater than distance criterion in specbond.dat file. you are right. I will correct this distance. Is my manner true (1 new entry in specbond.dat file and 2 new entries in aminoacids.rtp file)? If

[gmx-users] question

Dear Justin Since I want to consider the special bond between CD atom of GLU residue form peptide 1 and NZ atom of LYS residue from peptide 2, I did following steps: 1) I created 1 pdb file containing 2 peptides without any connection between aformentioned atoms (CD & NZ). I deleted OE2 atom of G

[gmx-users] question

Dear Justin Very thanks for your answer I should use my pdb file in which there is no bond between CD atom of GLU residue from peptide 1 and NZ atom of LYS residue from peptide 2. Creating new entry in specbond.dat file will consider this new bond. Is my vision true? Based on your answer, only t

Re: [gmx-users] question

In fact, I want to make an isopeptide bond. On Mon, May 11, 2015 at 11:04 PM, Andrew Bostick wrote: > Dear gromacs users > > I have experience in MD simulation of protein and peptides by gromos force > field. > > Now I am working on a new project in which I should connect two

[gmx-users] question

Dear gromacs users I have experience in MD simulation of protein and peptides by gromos force field. Now I am working on a new project in which I should connect two peptides (based on experimental data) to obtain one new peptide. This connection is as follows: CD atom of GLU residue from peptide

[gmx-users] question

Dear Gromacs users After I calculated the secondary structure of residues from 1 to 59 using do_dssp during 20 ns MD simulation, I used xpm2ps to show the picture with ps.m2p. y-axis is true but x- axis is very long. My ps.m2p file is as follows: ; Command line options of xpm2ps override the pa

[gmx-users] Cannot write trajectory frame; maybe you are out of disk space

Dear Justin Thanks for your reply. This problem can be solved by changing the parameters related to file system ? If I add another RAM to my computer system, my problem solves? Best regards -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing

[gmx-users] Cannot write trajectory frame; maybe you are out of disk space

Dear Mark I'm apologize. You are right. I should give more indication and information you to help me. I used chmod -R 777 directory containing pdb and mdp files. Then I did MD simulation again: (pdb2gmx ...> editconf > em ...> npt eq ...> md) My problem is in md step (md.trr file). 1)

[gmx-users] Cannot write trajectory frame; maybe you are out of disk space

Dear Mark I corrected file permission in my system using chmod -R 777 . But I encountered the same error: File input/output error: Cannot write trajectory frame; maybe you are out of disk space. Any help will highly appreciated -- Gromacs Users mailing list * Please search the archive at htt

[gmx-users] Cannot write trajectory frame; maybe you are out of disk space

Dear Mark Thanks for your reply. I googled file permission in linux OS. After that I did following steps: I created a directory entitled input. I put pdb and mdp files in the input directory. I used following command to change permission: chmod -R 777 input Now I will md simulation steps (pd

[gmx-users] Cannot write trajectory frame; maybe you are out of disk space

Dear Mark Thanks for your reply. I am beginner in linux and gromacs. How to rule out file permissions issues? Which command is true for doing this? Please guide me to solve this problem. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_List

[gmx-users] Cannot write trajectory frame; maybe you are out of disk space

Dear gromacs users I am doing md simulation on the a protein with 190 residues. I did minimization and equilibration without problem and error. But in production run step (last md simulation with 1500 steps), in step 650, I encountered with following error: File input/output error: Cann

[gmx-users] question about xvg file

Dear Tsjerk Thanks for your quick reply. I used awk '!($1%16)' file.xvg. It is very good. Since my xvg file is large. I want to have output in new xvg file (new.xvg) instead of screen. How to do this? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support

[gmx-users] question about xvg file

Dear gromacs users I did a MD simulation 1 years ago. Now, I have a dist.xvg file and I have not trajectory file (xtc). Time column in dist.xvg file is as follows: 0 4 8 12 16 . . . . 24984 24988 24992 24996 25000 I want to have this column as follows: 0 16 32 64 . . . . 24936 24952 24968 249

[gmx-users] binding delta G, H and S for ion-protein

Dear lloyd riggs Thanks for your consideratiuon You said " I have done this with a steered MD, using covarience " Please give me paper of your study (DOI or web page address) Best wishes -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] binding delta G, H and S for ion-protein

Dear Justin Very thanks for your guidance. You are right. Excuse me for my several questions. I am beginner in gromacs. If I want to calculate delta H IN potein-ions interaction, can I use g_energy? Is Enthalpy by g_energy exact? Is there a more appropriate tool for calculating delta H in grom

[gmx-users] binding delta G, H and S for ion-protein

Dear Justin Thanks for your answer. All of methods you mentioned ( PMF, TI, FEP, BAR) are used for calculating free energy (G). In addition to free energy (G), I want to calculate enthalpy (H) and entropy (S). Are you sure can I use above methods for calculating both of enthalpy (H) and entropy

[gmx-users] binding delta G, H and S for ion-protein

Dear groamcs users I want to calculate binding delta G. I know g_lie tool is used to calculate delta G for protein-ligand or enzyme-drug binding. Can I use g_lie tool o calculate delta G for binding some ions to one protein molecule? Generally, which toolS of gromacs are appropriate for delta

[gmx-users] enthalpy of ion + protein interaction

Dear gromacs users I want to obtain enthalpy of Cu2+ + my protein interaction. How to calculate that? Is g_energy appropriate for my case? Any help will highly appreciated. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_Lis

[gmx-users] genion

Dear Kalyan Thanks for your reply I want to use Zn2+ ions with my protein. There is Zn2+ ions in atomtypes.atp file of opls force field. But there is not Zn2+ ions in ions.itp file of of opls force field. Based on your answer, now, I can not use Zn2+ ions in genion tool. Is it true? But I used

[gmx-users] genion

Dear gromacs users In genion tool of gromacs, there are only Na and Cl ions. I want to add Zn2+ ions to my system. How to add these ions with special concentration? Any help will highly appreciated -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mai

Re: [gmx-users] question about gromacs

I used following line in mdp file: define = -DPOSRES_dopc -DPOSRES_chol Is my manner true? On Tue, Feb 4, 2014 at 5:09 PM, Andrew Bostick wrote: > Hi all > > My system contain dopc + cholesterol + water + drug molecules. > > I want to do MD simulation with position restra

[gmx-users] question about gromacs

Hi all My system contain dopc + cholesterol + water + drug molecules. I want to do MD simulation with position restraint on dopc and cholesterol molecules. I used following lines to obtain posre*.itp files: genrestr -f npt.gro -n index.ndx -o posre_dopc.itp genrestr -f npt.gro -n index.ndx -o

[gmx-users] question

Dear Jkrieger Thanks for your attention. I have index file containing 2 group which are my interest. Unfortunately, I am beginner in scripting and I have no long time. I should do this analysis as soon as possible. Please if you write such a script, send me it. Is g_rdf -cn appropriate for my c

[gmx-users] question

Dear all My aim of the number of neighbours (NS) is different from Neighbor Searching (nstlist and rlist) in mdp file. -- 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.

[gmx-users] question

Dear all I want to obtain number of atoms in a first group which are located in special distance of the second group. How to do this? Which tool of gromacs can do it? In fact, I want to obtain number of neighbours (NS). Any help will highly appreciated. -- Gromacs Users mailing list * Please s

[gmx-users] g_dist

Dear gromacs users I know g_dist tool calculates the distance between the centers of mass of two groups of atoms as a function of time. How to obtain average distances of the selected atoms form the bilayer midplane. In this case, one group is selected atoms, but another group? Is g_dist appropr

[gmx-users] MD simulation of lipid bilayers

Hi all I have a general question. In the MD simulation of lipid bilayers in papers, almost, most of the parameters calculated by gromacs is symmetric between top and bottom leaflet of bilayer. Is this symmetry obligatory? If in my case, for example density is not symmetry, is there problem? --

[gmx-users] question_gromacs

Dear Gromacs users I have following error when I do equilibration: There is no domain decomposition for 4 nodes that is compatible with the given box and a minimum cell size of 0.8875 nm Change the number of nodes or mdrun option -rcon or -dds or your LINCS settings. I tried all suggestios in ab

[gmx-users] question

Dear Justin Very thanks for your answers. Since you have more experience, can you tell me some modeling programs, web servers that will rebuild missing atoms, residues, or loops. After addition of missing atoms or residues, how to optimize new structure? Best wishes -- Gromacs Users mailing li

[gmx-users] question

Hi gmx users I am beginner in gromacs. Excuse me for my simple and ordinary questions. --- 1) In the most of tutorials and papers I read to now, for the simulation of a protein with a net charge (for example: -5 e