Dear All,
This is a general query regarding solvation of peptide in urea-water.
My method is to place the peptide in the box first, add urea molecules
using g_genbox and then solvate it using water molecules to maintain a
desired concentration.
There can be two approaches to this:
1) I can keep
Hello all,
I want to simulate methylamine with amino acid misture in CHARMM FF, so i
have created methylamine in mol2 format and created the .itp and .pdb files
from the CGenFF (which creates itp in CHARMM FF for GROMACS). and i have
included it in topology file also as:- #Include
I changed the order of .itp file and put the "topol_ATP.itp" ahead of
protein.itp . However, I got the following errors this time:
Fatal error:
Syntax error - File forcefield.itp, line 6
Last line read:
' 11 no 1.0 1.0'
Found a second defaults
Hi,
Gromos 54a7 force field has built-in topologies for some small molecules, like
ATP. In these topologies, many atoms have names of up to 5 letters, such as
AO1PA and AO2PB. However, PDB files seem do not support 5-letter atom names.
So, if I name an atom "AO2PB" in PDB, it will be
Dear All,
I am setting up a simulation of protein-ATP complex. I manually combined the
coordinates and topologies of the protein and ATP together, and ran editconf
and solvate successfully. However, when I ran grompp, errors occurred:
Syntax error - File forcefield.itp, line 4
Last line read:
Hi all,
I'm trying to calculate the number of residues (part of a residue) within a
distance (0.5 nm) to the surface of a molecule.
The molecule (MOL) is made up of 43 atoms.
The residues of interest are ASP (there's 36 of them in my system), but I'm
only interested in the COM between OD1 and
In the case of SHAKE constraint, there is no spring-like physics, like in
umbrella pulling. The distance between COMs evolves according to the rate
you set, but there is no COM oscillation around prescribed values, SHAKE
turns the distance into a solid stick.
Alex
On Thu, Jun 22, 2017 at 5:13
Hi All,
I was wondering if someone knows the difference between constraint versus
umbrella pulling. I have read the manual but I'm still not sure what this means.
1. Umbrella pulling: A harmonic potential is applied between the centers of
mass of two groups. Thus, the force is proportional
On Jun 21, 2017, at 2:32 AM, Leandro Bortot wrote:
>
> Have you compared the results of your calculation using the forces at
> different intervals? e.g. every 1, 10, 50, 100 steps ?
>
> As long as you use a not-so-large interval the result should be the same
> within
On 22/06/17 20:03, Sanim Rahman wrote:
Hello everyone,
I ran a short MD simulation with a 3dc ewald geometry to simulate a vacuum
slab at the top and bottom of my bilayer system. I equilibrated my system,
tripled the size of my system in the z-direction and then added the 3dc
geometry. My mdp
Hello everyone,
I ran a short MD simulation with a 3dc ewald geometry to simulate a vacuum
slab at the top and bottom of my bilayer system. I equilibrated my system,
tripled the size of my system in the z-direction and then added the 3dc
geometry. My mdp script is written as below:
title =
I've never used PLUMED, to be honest, so I don't know.
If ligands are salt ions or any other overall charged entities, I would
solvate the channel (with restraint, maybe) for essentially a production
run and apply an electric field "parallel" to the channel lumen, then
just visualize the
On 6/22/17 12:09 PM, ZHANG Cheng wrote:
Dear Gromacs,
I try to use this command to calculate RMSF:
echo 3 | gmx rmsf -s md_0_1.tpr -f md_0_1_noPBC.xtc -o rmsf_20-30ns.xvg -oq
bfac.pdb -res -b 2 -e 3
My simulation lasts for 30 ns, but I only want RMSF for the last 10 ns. It is
Dear Gromacs,
I try to use this command to calculate RMSF:
echo 3 | gmx rmsf -s md_0_1.tpr -f md_0_1_noPBC.xtc -o rmsf_20-30ns.xvg -oq
bfac.pdb -res -b 2 -e 3
My simulation lasts for 30 ns, but I only want RMSF for the last 10 ns. It is
mandatory to assign a reference frame, so I use
On 6/22/17 11:23 AM, Dilip H N wrote:
No, its not related to parameterization methodology. it is a different
question...
how can i identify the molecule as methylamine (for example) since in the
.rtp the molecule type is written as [MAM1]
[ MAM1 ]
[ atoms ]
N1 NG321-0.990 0
No, its not related to parameterization methodology. it is a different
question...
how can i identify the molecule as methylamine (for example) since in the
.rtp the molecule type is written as [MAM1]
[ MAM1 ]
[ atoms ]
N1 NG321-0.990 0
C1 CG3AM2 -0.060 1
HN1 HGPAM2
Hi,
On Thu, Jun 22, 2017 at 3:57 PM Diez Fernandez, Amanda <
amanda.die...@imperial.ac.uk> wrote:
> Hi Mark,
>
> Thanks.
>
> >mdrun will generally "make molecules whole" for -c, but otherwise doesn't
> >care. Implementing general triclininc 3D periodicity with domain
> >decomposition is a messy
On 6/22/17 9:53 AM, Sanim Rahman wrote:
Hello everyone,
I am curious if there is a feature in g_density that will allow me to
calculate the density of my system at every single frame. I am hoping to
track density change over time to calculate membrane thickness (peak to
peak of electron
Hi Mark,
Thanks.
>mdrun will generally "make molecules whole" for -c, but otherwise doesn't
>care. Implementing general triclininc 3D periodicity with domain
>decomposition is a messy business.
I am not using a triclinic unit cell (all angles are 90 in the input .pdb
file). Wouldn¹t the
Thank Justin.
Mark you are right. I did not think about to check the manual.
Thanks again.
> On 22 Jun 2017, at 15:51, Mark Abraham wrote:
>
> Hi,
>
> I'd start by looking in the documentation. Section 5.3.2 of the manual
> clearly suggests putting it in the
Hello everyone,
I am curious if there is a feature in g_density that will allow me to
calculate the density of my system at every single frame. I am hoping to
track density change over time to calculate membrane thickness (peak to
peak of electron density profile) and its standard deviation.
Hi,
I'd start by looking in the documentation. Section 5.3.2 of the manual
clearly suggests putting it in the ffnonbonded.itp file, which is where you
expected to find it at the start of this thread, right? :-)
Mark
On Thu, Jun 22, 2017 at 3:47 PM gozde ergin wrote:
>
On 6/22/17 9:47 AM, gozde ergin wrote:
Hey Justin,
I figured out how they calculated the sigma values.
Basically they just take the geometric mean of nitrogen and oxygen sigma and
epsilon from ffnonbed.itp file in OPLS-AA force field
and calculated the pairwise LJ for N-O interaction.
Now I
Hey Justin,
I figured out how they calculated the sigma values.
Basically they just take the geometric mean of nitrogen and oxygen sigma and
epsilon from ffnonbed.itp file in OPLS-AA force field
and calculated the pairwise LJ for N-O interaction.
Now I also try to add this information in my
Thanks! I reduced the number to 4, and it works:
gmx mdrun -v -dds 0.37 -nt 4
Cheers
Sergio Manzetti
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Tlf: +47
On 6/22/17 9:22 AM, Sergio Manzetti wrote:
Checked the link, nothing written here on rcon and dds...
"Thus it is not possible to run a small simulation with large numbers of
processors."
Google will help you find more suggestions.
-Justin
--
On 6/22/17 9:21 AM, Sergio Manzetti wrote:
Justin, I fixed the sim.mdp, however I realized I sent you the wrong mdp file,
the one that gave DNA minimization problem is the EM.mdp
Which is this:
define =
integrator = steep
emtol = 100.0
emstep = 0.001
nsteps = 10
; output frequency
Checked the link, nothing written here on rcon and dds...
Sergio Manzetti
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Midtun
6894 Vangsnes
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Org.nr. 911 659 654
Tlf: +47 57695621
[
Justin, I fixed the sim.mdp, however I realized I sent you the wrong mdp file,
the one that gave DNA minimization problem is the EM.mdp
Which is this:
define =
integrator = steep
emtol = 100.0
emstep = 0.001
nsteps = 10
; output frequency
nstxout = 50
nstvout = 0
nstfout = 0
On 6/22/17 9:16 AM, Sergio Manzetti wrote:
Hi, I have (also) a system of one molecule in water box of 3 3 3 dimensions,
the procedure goes well all the way till the simulation starts, getting:
Will use 20 particle-particle and 4 PME only ranks
This is a guess, check the performance at the
Hi, I have (also) a system of one molecule in water box of 3 3 3 dimensions,
the procedure goes well all the way till the simulation starts, getting:
Will use 20 particle-particle and 4 PME only ranks
This is a guess, check the performance at the end of the log file
OK, thanks for this!
Sergio Manzetti
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Midtun
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On 6/22/17 9:09 AM, Sergio Manzetti wrote:
I use the AMBER99SB-ILDN ff for a piece of DNA taken from the RCSB database.
Removed all waters and non-nucleic acid molecules, and everything seems fine.
The mdp settings are:
title = DNA in water stabilization
cpp = /lib/cpp
include = -I../top
I use the AMBER99SB-ILDN ff for a piece of DNA taken from the RCSB database.
Removed all waters and non-nucleic acid molecules, and everything seems fine.
The mdp settings are:
title = DNA in water stabilization
cpp = /lib/cpp
include = -I../top
define =
integrator = md
dt = 0.002
On 6/22/17 8:56 AM, Sergio Manzetti wrote:
HI, I use mdp for simulating with a 2fs time step, nstlist 10, rlist 1.2,
rcoulomb 1.2, rvdw 1.2, V-rescale, no P-coupling. Lincs on all bonds, still the
DNA system won't minimize .
What is your experience with DNA simulations and these settings?
Indeed. Thanks!
Sergio Manzetti
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On 6/22/17 8:31 AM, Nikhil Maroli wrote:
Thanks,
I have given the image of the system in the below link.
I thought if I can get Topology and Parameters for CNT alone would be
better to go with Charmm-gui. Since I can treat CNT as ligand and upload
the parameters will work with the server so
Thanks,
I have given the image of the system in the below link.
I thought if I can get Topology and Parameters for CNT alone would be
better to go with Charmm-gui. Since I can treat CNT as ligand and upload
the parameters will work with the server so in this aspects any suggestion?
like how to
THanks Justin.
Sergio Manzetti
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[ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ]
Midtun
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Hi,
The error message has a helpful URL that'll take you to the same advice
that we give several times a week on here :-)
Mark
On Thu, 22 Jun 2017 14:27 Sergio Manzetti
wrote:
> Thanks, Worked out. Now I got a note saying:
>
> NOTE 1 [file em.mdp]:
> The group
On 6/22/17 8:22 AM, Sergio Manzetti wrote:
Thanks, Worked out. Now I got a note saying:
NOTE 1 [file em.mdp]:
The group cutoff scheme is deprecated since GROMACS 5.0 and will be
removed in a future release when all interaction forms are supported for
the verlet scheme. The verlet scheme
Thanks, Worked out. Now I got a note saying:
NOTE 1 [file em.mdp]:
The group cutoff scheme is deprecated since GROMACS 5.0 and will be
removed in a future release when all interaction forms are supported for
the verlet scheme. The verlet scheme already scales better, and it is
compatible
On 6/22/17 8:14 AM, Sergio Manzetti wrote:
OK, now I treied writing Na Cl and not NA and CL and get:
This is what you did before, so naturally you get the same thing.
Na)
Warning: atom name 11966 in topol.top and dna_solv_NaCl.gro does not match (NA
- Na)
Warning: atom name 11967 in
OK, now I treied writing Na Cl and not NA and CL and get:
Na)
Warning: atom name 11966 in topol.top and dna_solv_NaCl.gro does not match (NA
- Na)
Warning: atom name 11967 in topol.top and dna_solv_NaCl.gro does not match (NA
- Na)
Warning: atom name 11968 in topol.top and dna_solv_NaCl.gro
On 6/22/17 6:59 AM, Nikhil Maroli wrote:
Dear Justin,
I have generated topology for CNT using gmx x2top. There is cyclic peptide
nanotube wrapped over the CNT (eight CP rings in equal intervals) otherwise
let's say, CNT is inserted into the Cyclic peptide nanotube. I wanted to
put the whole
On 6/22/17 7:30 AM, Sergio Manzetti wrote:
Hi, the procedure as defined by Juistin worked out well. However, a new problem
has occurred. At mdrun for the minimization, I get:
---
Program gmx mdrun, VERSION 5.1.2
Source code file:
Hi, the procedure as defined by Juistin worked out well. However, a new problem
has occurred. At mdrun for the minimization, I get:
---
Program gmx mdrun, VERSION 5.1.2
Source code file:
Hi,
On Wed, Jun 21, 2017 at 3:24 AM Adarsh V. K.
wrote:
> Dear all,
>
> *I used following command to extend a NPT simulation*
>
> 1) gmx convert-tpr -s npt.tpr -extend 500 -o tpxout.tpr
> gmx mdrun -deffnm tpxout -cpi npt.cpt -v
>
> but the analysis "
Hi,
I suggest you ask the authors of the tools, having checked their
documentation.
Mark
On Wed, Jun 21, 2017 at 6:36 AM Shivangi Agarwal <
shivangi.agarwal...@gmail.com> wrote:
> Hello all
>
> How to handle HS14 generated by ATB server in topology file?
>
>
> Regards
> --
> Gromacs Users
Hi,
On Thu, Jun 22, 2017 at 11:30 AM Emran Heshmati wrote:
> Hi all
> I run two simulations on a 16 aa peptide under the same conditions
> (forcefield, simulation duration, ...) except the solvent in one of
> the simulations was TFE instead of water. The potential energy in
Hi,
On Thu, Jun 22, 2017 at 11:05 AM Diez Fernandez, Amanda <
amanda.die...@imperial.ac.uk> wrote:
> Hi Mark,
> Thank you for your reply.
>
> It is exactly the opposite though:
OK, I understood the images the other way around, without titles.
> for output_coordinates.gro which is the
>
Hi,
I don't understand what you are asking. How does it relate to
parameterization methodology?
Mark
On Thu, Jun 22, 2017 at 7:20 AM Dilip H N wrote:
> Thank you for reply..
>
> But how can i identify the molecule as methylamine (for example) since in
> the .rtp the
Dear Justin,
I have generated topology for CNT using gmx x2top. There is cyclic peptide
nanotube wrapped over the CNT (eight CP rings in equal intervals) otherwise
let's say, CNT is inserted into the Cyclic peptide nanotube. I wanted to
put the whole system into the lipid bilayer. I was using
Hi all
I run two simulations on a 16 aa peptide under the same conditions
(forcefield, simulation duration, ...) except the solvent in one of
the simulations was TFE instead of water. The potential energy in the TFE
containing system was positive (about 14 Kj/mol), while in water
containing
Hi Mark,
Thank you for your reply.
It is exactly the opposite though: for output_coordinates.gro which is the
output from:
mdrun Š -c output_coordinates.gro
it seems like atoms are diffusing out of the box.
In the trajectory, I allow atoms to be seen to diffuse out of the box,
using -pbc
Hi Alex,
There is no confusion about the pulling that is only a preparation for
WHAM, but as you tell it you need to choose positions. These positions
could be choosen manually: if one choose to explore the static channel from
apo, then I'm agree, select the positions in the channel "in a bunch
I think your problem is solvable with enough perseverance, but there may
also be some confusion... The PMF calculation isn't based on the data
obtained from an actual pull: the pulling rate in those simulations is
set to zero. The reason for using pull code there is to pull (pun
intended) the
Hi everybody,
I would like to pull a ligand in a channel from my protein and calculate
the PMF with Umbrella sampling. This channel is probably not linear and
thus have to be defined. Too much colisions appears along a simple one axis
pulling and causing a catastrophic PMF calculation.
Currently
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