Dear all
I am trying to simulate a protein which a label (a small organic molecule)
is covalently attached to a cysteine. Worth to say there is no label in the
original pdb file of protein and it was attached to the Cys. using a
software.
Should I insert the label parameters into the conf.gro fil
>
> Yeah I have also found this page. Finally I did the conversion. I am
> currently testing the parameters.
>
Thank you Austin and Mark for your help
SA-
>
> --
>
> Message: 4
> Date: Wed, 20 Jul 2011 07:17:18 -0700 (PDT)
> From: "Austin B. Yongye"
> Subject: Re: [
Hi Faezeh,
You can modify the FF and add the Cys-label parameters to the *rtp and
*hdb files, such that pdb2gmx will be able to use them. Another why is
use the original pdb as a starting point and modify the output *gto,
*itp and *top files.
Just remember that in anycase, it is better to co
hi all,
I am new to GROMACS.I would like to know how we will simulate putting more
than two or more molecules of same proteins inside the box and do
simulation?Is there any possibility to replace 100 atoms or so of solvent
with proteins?
Please help.
Regards,
smriti
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gmx-users mailing listg
Hsin-Lin Chiang wrote:
於 2011/7/21 上午 03:19, gmx-users-requ...@gromacs.org 提到:
Hi everyone,
> > My pdb file is consist of two chains with one intra- two
> inter-disulfide bonds.
> So I used pdb2gmx in this way
> pdb2gmx -f protein.pdb -o protein.gro -p protein.top -n -q
-chainsep ter
>
smriti Sebastian wrote:
hi all,
I am new to GROMACS.I would like to know how we will simulate putting
more than two or more molecules of same proteins inside the box and do
simulation?Is there any possibility to replace 100 atoms or so of
solvent with proteins?
You can use editconf -center
On 21/07/2011 9:27 PM, smriti Sebastian wrote:
hi all,
I am new to GROMACS.I would like to know how we will simulate putting
more than two or more molecules of same proteins inside the box and do
simulation?Is there any possibility to replace 100 atoms or so of
solvent with proteins?
The sam
On 21/07/2011 4:26 PM, E. Nihal Korkmaz wrote:
Thanks but I already checked the literature. What I want to do is, to
be able to trace down the parameters in the nonbonded file like it can
be done for any version of gromos. There are slight changes among
different force fields and I'd like to be
On 21/07/2011 3:04 AM, Zhuyi Xue wrote:
Hi, there,
I have a edr file that looks containing about 2000 frames based on its
size as well as the result from gmxcheck:
frame: 75151040 (index 0), t: 150302.094
Reading energy frame 2 time 150320.000
Timesteps at t=150310 don't match (7.90
Hi folks
here I am with another kind of error, this time analysing my trajectory of
the rhombic dodecahedron dimeric system with g_cluster.
I used the following command:
g_cluster -f prot_boxdodfull_mol.xtc s prot_boxdodfull_molren.tpr -o
prot_boxdodfull_clust.xpm -sz prot_boxdodfull_clustsize.xvg
On 21/07/2011 11:38 PM, Anna Marabotti wrote:
Hi folks
here I am with another kind of error, this time analysing my
trajectory of the rhombic dodecahedron dimeric system with g_cluster.
I used the following command:
g_cluster -f prot_boxdodfull_mol.xtc s prot_boxdodfull_molren.tpr -o
prot_boxd
Hello,
I need parameters for DMPG membrane (G53a6 force field). Does anybody know
where I could find a tested parameter set and pdb file? If not, I believe I
could construct my own from e.g. Kukol A, Lipid Models for United-Atom
Molecular Dynamics Simulations of Proteins, DOI: 10.1021/ct8003468 by
> Please post a diff of the two topologies (the one that failed and the one
> that
> worked).
>
> -Justin
I use diff bash commend on the two top file and save to log file.
The different was long but they both have three inter-disulfide bond
There are 3973 lines in different log file.
I'm not
Hsin-Lin Chiang wrote:
**> Please post a diff of the two topologies (the one that failed and
the one that
> worked).
>
> -Justin
I use diff bash commend on the two top file and save to log file.
The different was long but they both have three inter-disulfide bond
There are 3973 lines in dif
Dear gmx users,
I have two short questions about generation of initial velocities in
simulations. If I want to run simulations at for example 400 K do I have to
alter the temperature for maxwell distribution settings? ( I mean
gen_temp= 400? )
gen_vel = yes
gen_temp
Juliette N. wrote:
Dear gmx users,
I have two short questions about generation of initial velocities in
simulations. If I want to run simulations at for example 400 K do I have
to alter the temperature for maxwell distribution settings? ( I mean
gen_temp= 400? )
Yes
Thanks Mark for suggestion, I'll try to do a simpler clustering method. In
the meantime, I only would like to add a further info: I pre-processed my
trajectory following someone's (Justin, IIRC) suggestion in a previous
message, using trjconv -pbc mol -ur compact. So, in my trajectory the
molecules
I suspect this is a bug, so I have filed an issue on redmine:
http://redmine.gromacs.org/issues/784
In a previous issue (http://redmine.gromacs.org/issues/544), the "-chainsep
interactive" option did not work, but now it does. Conversely, "-chainsep ter"
(which should also work in this case)
Hi Anna,
On Thu, Jul 21, 2011 at 5:11 PM, Anna Marabotti
wrote:
> Thanks Mark for suggestion, I'll try to do a simpler clustering method. In
> the meantime, I only would like to add a further info: I pre-processed my
> trajectory following someone's (Justin, IIRC) suggestion in a previous
> messa
Hi,
I am trying to calculate the binding energy of two molecules using the PMF
(Umbrella Sampling method) and Gromacs 4.0.
Some weeks ago I have written to the list because changing the number of
windows used in the Umbrella Sampling calculations different results were
obtained, and I was
>I suspect this is a bug, so I have filed an issue on redmine:
>
>http://redmine.gromacs.org/issues/784
>
>In a previous issue (http://redmine.gromacs.org/issues/544), the "-chainsep
>interactive" option did not work, but now it does. Conversely, "-chainsep ter"
>(which should also work in this c
Hsin-Lin Chiang wrote:
I suspect this is a bug, so I have filed an issue on redmine:
http://redmine.gromacs.org/issues/784
In a previous issue (http://redmine.gromacs.org/issues/544), the "-chainsep
interactive" option did not work, but now it does. Conversely, "-chainsep ter"
(which shoul
Rebeca García Fandiño wrote:
Hi,
I am trying to calculate the binding energy of two molecules using the
PMF (Umbrella Sampling method) and Gromacs 4.0.
Some weeks ago I have written to the list because changing the number of
windows used in the Umbrella Sampling calculations different result
Hi,
thanks a lot for your quick answer.
What I am trying to pull are two small peptides one from another (r_1 and r_2).
I did not understand very well your last suggestion: "...if you want reasonable
error bars you will not lots of well-converged data".
Do you mean I will need also more windows
Rebeca García Fandiño wrote:
Hi,
thanks a lot for your quick answer.
What I am trying to pull are two small peptides one from another (r_1
and r_2).
I did not understand very well your last suggestion: "...if you want
reasonable error bars you will not lots of well-converged data".
Oops, th
Justin A. Lemkul wrote:
Rebeca García Fandiño wrote:
Hi,
thanks a lot for your quick answer.
What I am trying to pull are two small peptides one from another (r_1
and r_2).
I did not understand very well your last suggestion: "...if you want
reasonable error bars you will not lots of well-
I am trying to achieve the binding energy of the dimer composed by the two
small cyclic peptides, to compare it with experimental. What advantages would I
have using 3D PMF instead only 1D for this calculation?
Thanks a lot!
Rebeca.
> Date: Thu, 21 Jul 2011 14:14:44 -0400
> From: jalem...
Rebeca García Fandiño wrote:
I am trying to achieve the binding energy of the dimer composed by the
two small cyclic peptides, to compare it with experimental. What
advantages would I have using 3D PMF instead only 1D for this calculation?
Intuitively, two molecules diffuse through soluti
OK,
I will try a dodecahedral box and also to extend my actual simulations.
Could you give me some advice about starting to learn about 3D PMF? I have not
seen this in the manual, and I have never used it before. I have only found
your tutorial about how to calculate PMF in Gromacs 4...
Thanks a
Rebeca García Fandiño wrote:
OK,
I will try a dodecahedral box and also to extend my actual simulations.
Could you give me some advice about starting to learn about 3D PMF? I
have not seen this in the manual, and I have never used it before. I
have only found your tutorial about how to calcul
Hello!
Why does the animation with ngmx not work always properly?
How can I save the animation in Linux?
Thanks!
Thomas
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Thomas Koller wrote:
Hello!
Why does the animation with ngmx not work always properly?
You'll have to define the symptoms better to get an answer to this. ngmx is a
very (very) rudimentary viewing program. You're better off with something more
sophisticated, like VMD or PyMol.
How
One potential problem you have is that as Justin mentioned your minimum
is not well defined and certain much less well sampled than the long
distances
windows. Small peptides (depends the size) may sample relevant phase
space to get reasonable convergence within 8 ns when free in solution;
in
Thanks for your answer.
My peptide has 6 residues and it is cyclic.
I calculated the errors through bootstrap, using this:
g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal -b 500 -n
Bootstrap 200
Are the pmfs aligned on the minimum distance value? Is that the value by
default?
Rebeca García Fandiño wrote:
Thanks for your answer.
My peptide has 6 residues and it is cyclic.
I calculated the errors through bootstrap, using this:
g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal -b 500
-n Bootstrap 200
Are the pmfs aligned on the minimum distance value
Well I do not know how g_wham is doing but it is likely that it does
align
different pmf obtained through the bootstraap the their minimum.
Justin just answered. The other alternative is to inverse your distances
with the data files.
On Jul 21, 2011, at 2:57 PM, Rebeca García Fandiño wrote:
Right. Even if you somehow force pdb2gmx to write a topology in this case, the
bonds are not correct and the termini are incomplete. That will hopefully be
resolved when the bug is fixed. For now, you have a workaround. Just use
"-chainsep interactive" and you will get a proper topology.
-Jus
Hi gmx-users,
I was trying to feed make_ndx with the non-interactive script, below
is my command:
The script called "choice.txt" contained:
ri 1-20
ri 21-40
ri 41-60
ri 61-80
ri 81-100
ri 101-120
Initially, I used the bash shell, then csh and tcsh, but in both the
cases it failed to produce the
You should issue a "q" command to save and quit. So "choice.txt" should look
like:
ri 1-20
...
...
ri 101-120
q
Cheers.
Terry
On Fri, Jul 22, 2011 at 1:53 PM, Chandan Choudhury wrote:
> Hi gmx-users,
>
> I was trying to feed make_ndx with the non-interactive script, below
> is my command:
>
Thanks Terry.
It worked.
Chandan
--
Chandan kumar Choudhury
NCL, Pune
INDIA
On Fri, Jul 22, 2011 at 12:00 PM, Terry wrote:
>
> You should issue a "q" command to save and quit. So "choice.txt" should look
> like:
> ri 1-20
> ...
> ...
> ri 101-120
> q
>
> Cheers.
> Terry
>
> On Fri, Jul 22, 20
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