Hi, there:
I found that in gromacs version 4.5.1, the residue ids are not ordered
consecutively as before in the .gro file. For example, if I have two
chains in the protein, then the residue ids will be ordered with
respect to each individual chain, rather than reordered to be a
complete
Dear Mark Abraham sir, thank you for your reply
i have edited my .top files in gromacs as u said when i run the ./grompp it
shows the error as follows
./grompp_d -f em.mdp -c spep_b4em.gro -p spep.top -o
Hi,
Yes.
Cubic spline interpolation means piecewise interpolation with third order
polynomials.
The terms says nothing about which derivatives are continuous.
Cubic spline interpolation is often used to interpolate between points where
only
the function value itself is provided and in that
Dear users,
I'm trying to create a box with a number (64) of small peptide molecules
(diphenylalanine) solved in ethanol for a Gromacs run with the Martini
coarse-grain force field.
I've created the box with the solute with the genbox -ci command: genbox -ci
FFMM_cg.pdb -nmol 64 -box 5 5 5 -o
NG HUI WEN wrote:
Dear Gmxusers,
I have noticed that energy minimization with gromacs (gromos G53a6
forcefield) had led to the distortion of sidechain planarity in my
protein model. Comparison of PROCEHCK results between the pre- and post
energy minimized structures have shown an
Try without -DFLEXIBLE.
See this message:
http://lists.gromacs.org/pipermail/gmx-users/2008-October/037571.html
Andreas
---
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On
Behalf Of NG HUI WEN
Sent: 20 September 2010 04:21
To:
Kukol, Andreas wrote:
Try without -DFLEXIBLE.
See this message:
http://lists.gromacs.org/pipermail/gmx-users/2008-October/037571.html
Doesn't -DFLEXIBLE only affect water, not the aromatic rings of the protein?
Don't the real problems come from running actual MD with -DFLEXBILE? In some
Pim Frederix wrote:
Dear users,
I'm trying to create a box with a number (64) of small peptide molecules
(diphenylalanine) solved in ethanol for a Gromacs run with the Martini
coarse-grain force field. I've created the box with the solute with the
genbox -ci command: genbox -ci FFMM_cg.pdb
Aswathy:
We can't tell if you did US correctly unless you post what you have
done. You must give more info and you must copy and paste the actual
input / .mdp parameters that you used.
As for if your PMF is correct, then we can never tell you that. You
can, however, ensure that your
I have a question regarding potential forms used in GROMACS:
Is it possible to use the standard functional forms for the potentials and
tabulated ones at the same time?
The system I'm looking at is a molecule on a surface. And ideally I want to
tabulate the surface interactions and treat the rest
Hi,
To avoid complex book keeping and parameter checking, you can only run with no
tabulated interactions
or all tabulated interactions.
But there are standard tables for LJ+Coulomb in the share/top directory.
I don't know what you mean with surface.
A uniform surface can be done with a
Hi all,
I'm trying to install Gromacs on BG/P following the instruction reported
here:
http://www.gromacs.org/Downloads/Installation_Instructions/GROMACS_on_BlueGene
I ran configure:
../configure --prefix=/bgp/userinternal/cin0644a/gromacs \
--enable-ppc-sqrt \
... and if I add the --enable-bluegene flag :
../../../../../src/gmxlib/nonbonded/nb_kernel_bluegene/nb_kernel_gen_bluegene.h,
line 163.21: 1506-1231 (S) The built-in function __fpsub is not valid
for the target architecture.
and more similar errors.
F.
On 09/20/2010 05:35 PM, Fabio Affinito
Hi,
I think you shouldn't enable fortran.
Berk
From: f.affin...@cineca.it
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] error on compilation on BlueGene/P
Date: Mon, 20 Sep 2010 17:50:48 +0200
... and if I add the --enable-bluegene flag :
Hi,
I have tried to add NaCl into my system in the 4.5.1 version to balance the
total charge, and used OPLS forcefield.
In the topol file file, it has CL- but no NA+. However, when I ran grompp_d, it
gave me the following error message:
Program grompp_d, VERSION 4.5.1
Source code file:
simon sham wrote:
Hi,
I have tried to add NaCl into my system in the 4.5.1 version to balance
the total charge, and used OPLS forcefield.
In the topol file file, it has CL- but no NA+. However, when I ran
grompp_d, it gave me the following error message:
Program grompp_d, VERSION 4.5.1
Hello,
I am simulating 2M urea in water with single methane (77 urea +
1926 water). I used genbox -ci -nmol to add the number of urea
molecules and then used genbox to add water molecules (as suggested in
the manual). When I tried to do energy minimization this is what I got :
On 2010-09-20 19.58, nishap.pa...@utoronto.ca wrote:
Hello,
I am simulating 2M urea in water with single methane (77 urea + 1926
water). I used genbox -ci -nmol to add the number of urea molecules and
then used genbox to add water molecules (as suggested in the manual).
When I tried to do
I did look at the plot, and it shows that the curve is smoothing right
under zero at -1.00e+05 but then why does the average potential show a
positive number? Shouldn't that number be negative as well?
Quoting David van der Spoel sp...@xray.bmc.uu.se:
On 2010-09-20 19.58,
Hi,
I have figured the problem. Can't use NA+/CL- in the latest version, and have
to use NA/CL at least in OPLS.
Best,
Simon
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
Running several free energy perturbation (FEP) runs to further understand how I should set up my larger production runs and I keep getting errors that I cannot find in the gmx-user email or anywhere specifically online.
Error 1:
I get this error on three of
Hi,
Could you file a bugzilla?
And what do you mean with -dlb on?
on is not an option, the options are: auto, yes, no
Thanks,
Berk
Date: Mon, 20 Sep 2010 12:22:18 -0700
From: musta...@onid.orst.edu
To: gmx-users@gromacs.org
Subject: [gmx-users] Getting some interesting errors.
Yes -dlb no not on and I will file a bugzilla. Thanks again Berg Hess.
TJ Mustard
On September 20, 2010 at 8:38 PM Berk Hess g...@hotmail.com wrote:
Hi,
Could you file a bugzilla?
And what do
Dear Justin:
Thanks a lot for your reply.
I indeed have missing residues in the second chain. However, when I
try pdb2gmx -renum, it renumbers the second chain starting from 1,
rather than starting from 817(Nres_1st+1).
Thanks,
Bin
=
816VAL
BIN ZHANG wrote:
Dear Justin:
Thanks a lot for your reply.
I indeed have missing residues in the second chain. However, when I try
pdb2gmx -renum, it renumbers the second chain starting from 1, rather
than starting from 817(Nres_1st+1).
To get consecutive numbering, you may have to
(identical with version
4.5 and the most recent git with release-4-5-patches):
pdb2gmx -f struct.pdb
...
---
Program pdb2gmx, VERSION 4.5.1-20100920-03d181e
Source code file: pdb2gmx.c, line: 655
Fatal error:
Atom OXT in residue CRO 331
received the
following error (identical with version 4.5 and the most recent git with
release-4-5-patches):pdb2gmx -f struct.pdb ...
--- Program pdb2gmx,
VERSION 4.5.1-20100920-03d181e Source code file: pdb2gmx.c, line: 655
Fatal
error (identical with version 4.5 and the most
recent git with release-4-5-patches):
pdb2gmx -f struct.pdb
...
---
Program pdb2gmx, VERSION 4.5.1-20100920-03d181e
Source code file: pdb2gmx.c, line: 655
Fatal error:
Atom OXT in residue
the following error (identical with version 4.5 and the most
recent git with release-4-5-patches):
pdb2gmx -f struct.pdb
...
---
Program pdb2gmx, VERSION 4.5.1-20100920-03d181e
Source code file: pdb2gmx.c, line: 655
Fatal error
Hi,
IIRC GROMACS has done something radical to FORTRAN inner loops (like removing
them) since those instructions were written. Removing --enable-fortran will
make your symptoms go away. The C inner loops will be fine, should you ever be
running mdrun on the front end nodes.
... and if I add
This may very well be a simple problem, but I have found little in the way
of documentation that helped me get it to work:
I'd like to form a box (4x6x4 nm^3) filled with 3200 water molecules. I'd
like to use the water model specified in sw.itp (polarizable flexible). In
the working directory I
Eric Shamay wrote:
This may very well be a simple problem, but I have found little in the
way of documentation that helped me get it to work:
I'd like to form a box (4x6x4 nm^3) filled with 3200 water molecules.
I'd like to use the water model specified in sw.itp (polarizable
flexible).
Is there something about the water molecule that is different to any
standard H2O? If not, then simply use:
genbox_d -cs -box 4.0 6.0 4.0 -maxsol 3200
Catch ya,
Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceutical Sciences, Monash University
381
with version 4.5 and the most
recent git with release-4-5-patches):
pdb2gmx -f struct.pdb
...
---
Program pdb2gmx, VERSION 4.5.1-20100920-03d181e
Source code file: pdb2gmx.c, line: 655
Fatal error:
Atom OXT in residue CRO
Hi
Thanks a lot for the suggestions.
I removed -DFLEXIBLE this time but it still didn't work unfortunately. I
started off with 0 distorted planar group and ended up with 38 after
minimization (same as before).
Justin, the values were as below when the minimization converged to
machine
Hi There,
I am trying to run molecular dynamics on a drug-enzyme complex using
amber force field. I have done it earlier using gromos FF using
drug-enzyme tutorial, I dont know if the parameter set (.mdp file)
will be same or different while using AMBER FF.
Any insight/comments into the matter may
First, you have to develop parameter for your molecule withing Amber. Then
you have to create .prmtop and .inpcrd files for your molecule, and than you
can convert the Amber topology to Gromacs topology. You will need AmberTools
and a script called amb2gmx.pl.
Following links would be helpful for
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