On 21/06/2011 4:33 PM, bharat gupta wrote:
So, after adding 1 NA ion, I started with energy mimization, but I am
getting the following error after md run command :-
Please search for help first.
http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings
Mark
Step=1, Dmax
On 21/06/2011 4:15 PM, bharat gupta wrote:
I fixed it ... but now after using the command : grompp -f em.mdp -c
solv.gro -p topol.top -o ions.tpr
I am getting a charge of -9.71e-01
Since the charge has to be in whole number, what shall I do in this
case. (The ligand that I am using is p
Dear users,
When are checking the cosine content of a PC, (Pls. Correct me if I am
wrong)
This is the command we use -
"g_analyze -f .xvg -cc .xvg"
and for first PC output says -
Cosine content of set 1 with 0.5 periods: ---
for nth PC also it says -
Cosine content of set 1 with 0.5 periods:
So, after adding 1 NA ion, I started with energy mimization, but I am
getting the following error after md run command :-
Step=1, Dmax= 1.0e-02 nm, Epot= 1.36889e+09 Fmax= 1.97591e+11, atom=
1248
Step=2, Dmax= 1.2e-02 nm, Epot= 5.46814e+07 Fmax= 3.57239e+09, atom=
972
Step=3, Dmax= 1
On 21/06/2011 3:43 PM, Kavyashree M wrote:
Sir,
I am extremely sorry for this question again :(
but I wanted to know this violation exists only in
first 50ns but after that even though there appears
to be a point of violation its only 1.39nm which is
o0.01nm less than the cut off which I ho
I fixed it ... but now after using the command : grompp -f em.mdp -c
solv.gro -p topol.top -o ions.tpr
I am getting a charge of -9.71e-01
Since the charge has to be in whole number, what shall I do in this case.
(The ligand that I am using is phosphotyrosine)
On Tue, Jun 21, 2011 at 2:13
Dear all,
This may sound stupid, but just to make sure that I am right track about
implicit solvent simulations, the set up involves
pdb2gmx
editconf
grompp
I mean, we still need to define the box dimensions by editconf and apply
periodicity, right?
Besides, what type of ensemble would be a good
Sir,
I am extremely sorry for this question again :(
but I wanted to know this violation exists only in
first 50ns but after that even though there appears
to be a point of violation its only 1.39nm which is
o0.01nm less than the cut off which I hope does
not cause serious trouble (as the min
On 21/06/2011 3:03 PM, bharat gupta wrote:
Now I changed the .top file in this way and I am getting this error now :-
change :- ; Include forcefield parameters
#include "charmm27.ff/forcefield.itp"
;Include ligand topology
#include "PTR.itp"
[ moleculetype ]
; Namenrexcl
Protein_ch
Now I changed the .top file in this way and I am getting this error now :-
change :- ; Include forcefield parameters
#include "charmm27.ff/forcefield.itp"
;Include ligand topology
#include "PTR.itp"
[ moleculetype ]
; Namenrexcl
Protein_chain_A 3
=
error:-
On 21/06/2011 2:51 PM, bharat gupta wrote:
ok now I am doing the things again and here is the result of output of
each command till adding ions. At the time of executing the command
grompp for reading em.mdp file for ions.tpr generation, I am getting
the following error:-
Fatal error:
Syntax
ok now I am doing the things again and here is the result of output of each
command till adding ions. At the time of executing the command grompp for
reading em.mdp file for ions.tpr generation, I am getting the following
error:-
Fatal error:
Syntax error - File PTR.itp, line 7
Last line read:
'[
Dear Tsjerk
thanks for your attention.
larger radius of gyration, more surface. and smaller radius of
gyration, less surface.
I want to obtain solvent accessible surface area using g_sas.
g_sas -f *.xtc -s *.tpr -n *.ndx -o -or -oa.
I will obtain three output files containing: area.xvg, resar
bharat gupta wrote:
Hi,
In addition to my last mail, I am also getting another error during the
minimization step. I made the changes in em_real.mdp file for my sytem
but its showing the error that "ource code file: readir.c, line: 1316
Fatal error:
Group PTR not found in indexfile.
"
I
On 21/06/2011 12:05 PM, bharat gupta wrote:
Hi,
Initially while preparing the structure , -2 charge was there on the
protein. Next, after adding the ligand and executing grompp statement
It showing -9.9 charge.
See http://www.gromacs.org/Documentation/Floating_Point_Arithmetic,
which may be
Go back through your procedure, repeating it again, step by step. Take note of
number of atoms, charges etc as you go. And answer the other questions I put
to you previously.
Catch ya,
Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceutical Sciences, Monash Un
I checked the .gro file , in that only 9 NA are mentioned.. also during the
minimization step I am getting the following error:-
step 100: Water molecule starting at atom 85940 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and c
You need to work out exactly why you have the mis-match, something is screwy.
Something that you are doing does not add up.
What is the charge on the ligand? Appears to be -7.
Why when you add 9 Na+ do you then end up with a charge of +8? Seems that you
have actually added 17 sodiums from tho
Hi,
In addition to my last mail, I am also getting another error during the
minimization step. I made the changes in em_real.mdp file for my sytem but
its showing the error that "ource code file: readir.c, line: 1316
Fatal error:
Group PTR not found in indexfile.
"
also the charge on the system
Hi,
Initially while preparing the structure , -2 charge was there on the
protein. Next, after adding the ligand and executing grompp statement It
showing -9.9 charge. So I added 9 sodium ions. but still its showing +8
charge on the system. what shall I do in this case ??
--
Bharat
Ph.D. Candidat
On 21/06/2011 8:30 AM, Thomas Evangelidis wrote:
Dear GROMACS users,
I've read in the manual and in previous posts that NMR chemical shifts
can be computed from phi/psi angles. However, it was unclear whether
the inverse is possible with GROMACS, namely to use chemical shifts
(1H, 13C, 15N) a
Dear GROMACS users,
I've read in the manual and in previous posts that NMR chemical shifts can
be computed from phi/psi angles. However, it was unclear whether the inverse
is possible with GROMACS, namely to use chemical shifts (1H, 13C, 15N) as
restraints (possibly as secondary structure restrain
Gavin Melaugh wrote:
Hi all
I have read the manual and the recent JCTC paper on g_wham, and I was
wondering how to actually get the error bars on the profile.xvg file
outputted from g_wham.
A suitable combination of g_wham -bs-method -nBootstrap, etc. See g_wham -h.
-Justin
--
===
Kavyashree M wrote:
Dear users,
I ran 100ns simulation for 4 proteins, 3 of them were
non covalent dimers in solution, but only 1 is a covalent
dimer connected by a disulphide bridge. I used monomers
to run the job.
Only in the case of covalent dimer I was getting severe
minimum imag
Rebeca García Fandiño wrote:
Dear Justin,
my name is Rebeca and I am a postdoctoral student in Santiago de
Compostela University. Sorry for disturbing you to your personal mail, I
have tried to post to the Gromacs-list first, but I did not get any answer.
I was traveling and not paying much
On 21/06/2011 2:46 AM, Du Jiangfeng (BIOCH) wrote:
Dear Gromacs Users,
It comes to me with million problems per day during I am using gromacs. :(
Computational chemistry is rarely easy. The tasks are complex and
demanding, even when the software is mature and the documentation well
written...
On 21/06/2011 2:44 AM, udaya kiran marelli wrote:
Dear GROMACS users,
I have generated a 4*4*4 octahedral DMSO box containing 64 molecules
(Charmm all-atom force field) which need to be NVT equilibrated in
order to pass it for usage in genbox. Could one of you provide info
on how to do the N
On 21/06/2011 2:10 AM, E. Nihal Korkmaz wrote:
What would you suggest as a short time step? I was using 0.002 ps.
I'd suggest starting with maybe 100ps of 0.0005 ps time steps, but
that's probably overkill.
And just to make sure, would 5 ns of equilibration be enough for a
~110 amino acid l
Dear Gromacs Users,
It comes to me with million problems per day during I am using gromacs. :(
Maybe you are the right persons i should ask about coarse grained protein-lipid
simulation. Right now I have a system with a bilayer (DOPCs) and a protein
(Histone). After EM simulation, it worked quite
Dear GROMACS users,
I have generated a 4*4*4 octahedral DMSO box containing 64 molecules (Charmm
all-atom force field) which need to be NVT equilibrated in order to pass it
for usage in genbox. Could one of you provide info on how to do the NVT and
periodic boundary equilibration to remove the re
Dear Mark Abraham,
Thank you for your support. However, I have edited the N-terminus in -hdb
file so as too include a HN atom for the specific residue and it worked.
regards,
Uday..
On Fri, Jun 17, 2011 at 10:29 PM, wrote:
> Send gmx-users mailing list submissions to
>gmx-users@gromac
What would you suggest as a short time step? I was using 0.002 ps. And just
to make sure, would 5 ns of equilibration be enough for a ~110 amino acid
long protein?
Thanks,
Nihal
On Mon, Jun 20, 2011 at 7:41 AM, Mark Abraham wrote:
> **
> On 20/06/2011 3:29 PM, E. Nihal Korkmaz wrote:
>
> I also
I've had bad luck with parallel minimizations, particularly for the
4.0 series of GROMACS. Either domain decomposition fails or numeric
problems appear (SETTLE failures and the like), but disappear when run
serially. Minimization tends to be low cost compared to equilibration
anyway, so my soluti
Good afternoon,
I'm using GROMACS version 4.0.5. My simulation system is a double
stranded DNA (51 nucleotides) in a water (TIPI3P type) box, defined as
0.9 A from the DNA, with 100 Na ions to neutralize the system. The
sequencial commands used were:
1) pdb2gmx -f dsDNA.pdb -p dsDNA.top -o
On 20/06/2011 3:29 PM, E. Nihal Korkmaz wrote:
I also checked the output of the minimization:
Steepest Descents converged to machine precision in 402 steps,
but did not reach the requested Fmax < 10.
Potential Energy = -1.81875038188621e+04
Maximum force = 3.20769543152855e+02 on atom 331
Dear Tsjerk
thanks for your attention.
larger radius of gyration, more surface. and smaller radius of
gyration, less surface.
I want to obtain solvent accessible surface area using g_sas.
g_sas -f *.xtc -s *.tpr -n *.ndx -o -or -oa.
I will obtain three output files containing: area.xvg, resar
Hi Shahab,
> I want to know exactly how do radius of gyration of protein from free state
> to complex state change .
> Rg increased od decreased?
That depends on the protein. Some will, e.g., close or fold upon
binding, while others may open up, or unfold.
> I want to know my data [ In my simula
Dear Tsjerk
thanks for your reply.
in paper 1 :
larger radius of gyration, less compact, more surface
in paper 2:
(smaller radius of gyration; not stated explicitly), more compact, less surface.
in paper 3:
[Journal of Structural Biology 156 (2006) 537–545]
Overall, the GBD appears a little
Hi all
I have read the manual and the recent JCTC paper on g_wham, and I was
wondering how to actually get the error bars on the profile.xvg file
outputted from g_wham.
Many Thanks
Gavin
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Pleas
Hey Shahab,
What's the contradiction?
> [ Furthermore, INT–DBD appears less compact in the complex, as far as the
> radius of gyration increases and more molecular surface is exposed to the
> solvent (Table 1). ]
larger radius of gyration, less compact, more surface
> [ Furthermore, according t
Dear all
I am studying md simulation of free protein and protein-ligand and
protein-dna complex.
In my simulation systems, the average of radius of gyration in free protein
is 2.31 and for protein in complex is 2.58.
I know the radius of gyration is measurement of compactness of the protein
as
s
Hello,
I am trying to obtain the PMF from Umbrella Sampling of the process of
separating two monomers of a dimer.
I am following the tutorial
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/05_pull.html
and I have a doubt:
In this tutorial the generation of config
Well, there must be some thing some where that you did the wrong way :))
You should try again from the start and may be try to post on the
Martini website forum
www.cgmartini.nl
XAvier
On Jun 20, 2011, at 9:41 AM, Naba wrote:
Dear Users/Developers
I am trying to set a coarse-grained MD f
Please ignore my last question, I have found the answer using the g_wham
-h option
Cheers
Gavin
Gavin Melaugh wrote:
> Hi all
>
> I have generated a PMF curve over 15 ns. Does g_wham have a facility
> whereby I can calculate the PMF over say 7 ns, to check for convergence.
> There doesn't seem t
Hi all
I have generated a PMF curve over 15 ns. Does g_wham have a facility
whereby I can calculate the PMF over say 7 ns, to check for convergence.
There doesn't seem to be anything in the manual.
Many thanks
Gavin
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mai
Dear Users/Developers
I am trying to set a coarse-grained MD for the same protein (1UBQ.pdb)
therein the MARTINI tutorial (
http://md.chem.rug.nl/cgmartini/index.php/tutorial).
After the solvation by water-1bar-303K.gro I tried to minimize the system
but it gives the following weired results.
gro
Dear users,
I ran 100ns simulation for 4 proteins, 3 of them were
non covalent dimers in solution, but only 1 is a covalent
dimer connected by a disulphide bridge. I used monomers
to run the job.
Only in the case of covalent dimer I was getting severe
minimum image violation ie. out of 500
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