Hello,
I want concatenate two trajectories which have same number of frames
and they have written for identical time period i.e. the simulation
time is same for both the trajectories(for my case 100ns each) the
only thing differ is the temperature of simulation.
Please suggest me whether the below
Hi
can any one help me in sorting out the file conversion error,
when using PRODRG server for converting pdb - gromacs topology format for
small molecule.
the error message displayed in gromacs was
Atomtype CH3 not found (while using amber99 FF)
or
Atomtype CH1 not found (while using GMX)
or
A
Thank you Austin, for the clarification,
So my questions are: how to convert it in the gromacs format ? Is it correct
to use the absolute value of the multiplicity in my parameters and use the
negative values of barrier heights when they are exist in the AMBER
parameters? Since, I have noticed tha
Dear allI am trying to run a simulation of a dimer including a zinc finger
using Gromacs 4.5.3. I have gone through the documentation and searched the
forums but could not find a specific answer to my problem.
In order to produce the initial topology (top) and coordinate (gro) files for
the sim
subramaniam boopathi wrote:
dear sir,
i was doing gromacs when i run pdb2gmmx i got following error
that is some atom missing
You need to provide an intact structure to pdb2gmx. You will have to use other
software to replace the missing atoms. There are various programs that can
Sajad Ahrari wrote:
hi dear users
is there any command in gromacs to determine mass center of a protein? I
mean to find out witch atom or residue stands for mass center.
No, but you can use g_traj -com to extract the coordinates of the center of
mass. From there, you can probably determine
bipin singh wrote:
Hello,
I want concatenate two trajectories which have same number of frames
and they have written for identical time period i.e. the simulation
time is same for both the trajectories(for my case 100ns each) the
only thing differ is the temperature of simulation.
Please sugge
Parthiban Marimuthu wrote:
Hi
can any one help me in sorting out the file conversion error,
when using PRODRG server for converting pdb - gromacs topology format
for small molecule.
the error message displayed in gromacs was
Atomtype CH3 not found (while using amber99 FF)
or
Atomtype CH1 n
DAVID DE SANCHO wrote:
Dear all
I am trying to run a simulation of a dimer including a zinc finger using
Gromacs 4.5.3. I have gone through the documentation and searched the
forums but could not find a specific answer to my problem.
In order to produce the initial topology (top) and coordi
Yes It is workingbut I have not tried that, what would be the
difference if I don't give -cat option
On Wed, Jul 20, 2011 at 16:16, Justin A. Lemkul wrote:
>
>
> bipin singh wrote:
>>
>> Hello,
>>
>> I want concatenate two trajectories which have same number of frames
>> and they have
bipin singh wrote:
Yes It is workingbut I have not tried that, what would be the
difference if I don't give -cat option
If the times are the same, then the second trajectory would have overwritten the
first. Please read the first paragraph of trjcat -h.
-Justin
On Wed, Jul
Thanks Sir,
I understood...
On Wed, Jul 20, 2011 at 16:46, Justin A. Lemkul wrote:
>
>
> bipin singh wrote:
>>
>> Yes It is workingbut I have not tried that, what would be the
>> difference if I don't give -cat option
>>
>
> If the times are the same, then the second trajectory would
Hi all,
I was wondering if there is any way to take an MDrun done on Gromacs 4.0.7
and converting it so it is compatible with Gromacs 4.5.4.
Best,
Gideon
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Please search the archive at
http://ww
> So my questions are: how to convert it in the gromacs format ?
I haven't done AMBER to GROMACS conversions. But a google search led me to this
page. It's just a matter of knowing the different formats.
http://ffamber.cnsm.csulb.edu
> Is it correct to use the absolute value of the multiplicity
גדעון לפידות wrote:
Hi all,
I was wondering if there is any way to take an MDrun done on Gromacs
4.0.7 and converting it so it is compatible with Gromacs 4.5.4.
You will have to recreate the .tpr file since the file format has changed.
Trajectory and coordinate files are version agnostic
Justin A. Lemkul wrote:
גדעון לפידות wrote:
Hi all,
I was wondering if there is any way to take an MDrun done on Gromacs
4.0.7 and converting it so it is compatible with Gromacs 4.5.4.
You will have to recreate the .tpr file since the file format has
changed. Trajectory and coordinate
Hi, all!
Is any polarizable water models are available in ITP format? Or may be I
should prepare .itp from some articles? In recent mail archive I've found
some mentions about SWFLEX-AI model. Also I've found van der Spoel's
article. May be somebody have ready .itp files of some models?
Thanks be
On 20/07/2011 7:33 PM, sa wrote:
Thank you Austin, for the clarification,
So my questions are: how to convert it in the gromacs format ? Is it
correct to use the absolute value of the multiplicity in my parameters
and use the negative values of barrier heights when they are exist in
the AMBER
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
(I have deleted the TER and OXT lines of A-chain.)
I'm not sure if I need to use -ter here, I don't
> Is any polarizable water models are available in ITP format? Or may be I
> should prepare .itp from some articles? In recent mail archive I've found
> some mentions about SWFLEX-AI model. Also I've found van der Spoel's
> article. May be somebody have ready .itp files of some models?
>
There sho
Hsin-Lin Chiang wrote:
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
(I have deleted the TER and OXT lines of A-chain.)
I'm not sure if I nee
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 (7.90625, 10)
Reading energy frame 2000 time
Hi gmx-users,
Is there a way to create a branched polyhistidine chain using gromacs,
instead of a straight chain?
Thanks,
SN
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Hi,
If you have time, I am wondering if you can help me understand some parts
about .itp files. Before I ask my questions, though, I will paste below a
few relevant files (or parts of files). My system consists of 1000 SPC/E
water molecules in a cubic box of edge length 4.71 nm. I am using the
shivangi nangia wrote:
Hi gmx-users,
Is there a way to create a branched polyhistidine chain using gromacs,
instead of a straight chain?
There is limited support for branched chains via pdb2gmx. The only way to
introduce a branch point is by using specbond.dat.
http://www.gromacs.o
Andrew DeYoung wrote:
Hi,
If you have time, I am wondering if you can help me understand some parts
about .itp files. Before I ask my questions, though, I will paste below a
few relevant files (or parts of files). My system consists of 1000 SPC/E
water molecules in a cubic box of edge length
Dear all,
I am trying to simulate a protein in urea solution. I used *genbox -cp
protein_in_box.gro -cs urea+h2o.gro -o out.gro -p topology* but the
resulting topology doesn't contain any information on urea nor the atoms of
urea. I also tried adding ureas on the protein with *-ci urea_single.gro
E. Nihal Korkmaz wrote:
Dear all,
I am trying to simulate a protein in urea solution. I used /*genbox -cp
protein_in_box.gro -cs urea+h2o.gro -o out.gro -p topology*/ but the
resulting topology doesn't contain any information on urea nor the atoms
of urea. I also tried adding ureas on the p
>> Is any polarizable water models are available in ITP format? Or may be I
>> should prepare .itp from some articles? In recent mail archive I've found
>> some mentions about SWFLEX-AI model. Also I've found van der Spoel's
>> article. May be somebody have ready .itp files of some models?
>>
>The
Alex [comcon1] Nesterenko wrote:
Is any polarizable water models are available in ITP format? Or may be I
should prepare .itp from some articles? In recent mail archive I've found
some mentions about SWFLEX-AI model. Also I've found van der Spoel's
article. May be somebody have ready .itp files
Dear all,
I was trying to see the LJ parameters for SPC/E water in Charmm27.ff
implementation in Gromacs. In the ffnonbonded.itp file i can see parameters
for TIP3P, TIP4P, SPC but not for SPC/E. Does SPC/E use the same parameters
with SPC? (but the charges listed in the ffnonbonded.itp is differe
Hi Justin,
Thanx for the suggestion. This is how my topology looks like with the
strong position restraint included for the protein:
; Include forcefield parameters
#include "gromos53a6.ff/forcefield.itp"
; Include chain topologies
#include "complex6_Protein_chain_X.itp"
#include "complex6_Prote
Sweta Iyer wrote:
Hi Justin,
Thanx for the suggestion. This is how my topology looks like with the
strong position restraint included for the protein:
; Include forcefield parameters
#include "gromos53a6.ff/forcefield.itp"
; Include chain topologies
#include "complex6_Protein_chain_X.itp"
#i
>>> Is any polarizable water models are available in ITP format? Or may be I
>>> should prepare .itp from some articles? In recent mail archive I've found
>>> some mentions about SWFLEX-AI model. Also I've found van der Spoel's
>>> article. May be somebody have ready .itp files of some models?
>>>
Hi, Alex.
You wrote 21 July 2011, 8:06:11:
>>> Is any polarizable water models are available in ITP format? Or may be I
>>> should prepare .itp from some articles? In recent mail archive I've found
>>> some mentions about SWFLEX-AI model. Also I've found van der Spoel's
>>> article. May be somebo
On 21/07/2011 12:59 PM, E. Nihal Korkmaz wrote:
Dear all,
I was trying to see the LJ parameters for SPC/E water in Charmm27.ff
implementation in Gromacs. In the ffnonbonded.itp file i can see
parameters for TIP3P, TIP4P, SPC but not for SPC/E. Does SPC/E use the
same parameters with SPC? (but
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
> (I have deleted the TER
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 able to find that. When I find where it reads
spc/
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