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
Dear Justin,
Thanks for your answer. Does ATB need no correction?
Best,
Andrew
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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
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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
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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
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
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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
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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
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
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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)
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
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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
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
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:
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
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
Also, I have located dssp program in /usr/local/bin
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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
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
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
Dear gromacs users,
How to calculate viscosity and surface tension in the simulation of some
small molecules in the box of water.
Best,
Andrew
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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
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
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
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,
Dear all
Is there amber99bsc0 in gromacs default force fields?
Best,
Andrew
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Dear gromacs users,
For neutralizing the simulation system, can I use K+ ions instead of NA+?
Best,
Andrew
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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
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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.
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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
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 -99023.460938
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
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
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
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)
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
http://www.gromacs.org/Documentation/Installation_Instructions_5.0?highlight=installation#TOC
instruction.
When
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?
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Dear Tsjerk
I used pdb2gmx -f be_near.pdb -ignh -merge
Thanks in advance.
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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)?
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
In fact, I want to make an isopeptide bond.
On Mon, May 11, 2015 at 11:04 PM, Andrew Bostick andrew.bosti...@gmail.com
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
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
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
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)
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
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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
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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.
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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
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?
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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
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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
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.
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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
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
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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.
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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
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?
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