for the neutral chromophore or protonated one ??
>
>
> On Thu, Jun 23, 2011 at 4:29 PM, Ramachandran G wrote:
>
>> yes!
>>
>>
>> On Thu, Jun 23, 2011 at 12:26 AM, bharat gupta
>> wrote:
>>
>>> these are in continuity I mean for the ffbonded.it
yes!
On Thu, Jun 23, 2011 at 12:26 AM, bharat gupta wrote:
> these are in continuity I mean for the ffbonded.itp file
>
> On Thu, Jun 23, 2011 at 4:21 PM, Ramachandran G wrote:
>
>> more parameters - ffbonded.itp
>> NBCT 10.1444294553.6
>&
On Thu, Jun 23, 2011 at 12:18 AM, Ramachandran G wrote:
> For ffbonded.itp, i added the following. (you need to be carefull here
> since i cooked upto the force constants)
> C CCCBCA9 180.0 4.309 1
> NBCCC O 9 180.0 4.309 1 ;
>
CC C4 180.04.1840 2
NBCCCCT 4 180.04.1840 2
CACBCA CA 4 180.04.1840 2
CAHACA CA 4 180.04.1840 2
; added to test
N CT CH4 180.04.1840 2
On Thu, Jun 23, 2011 at 12:13 AM, Ramachandran G wrote
For the GFP chromophore i name residue as CRIH.
1. aminoacids.rtp
CB2 CB 0.019103 1
CA2 CC-0.026635 2
N2 NB-0.436463 3
C1 CC 0.302706 4
N3 NB-0.541478 5
C2 C 0.563844
ng fine then I think you can deposit it in User contributions in
> gromacs repository...
>
>
> On Thu, Jun 23, 2011 at 2:38 PM, Ramachandran G wrote:
>
>> Why you are doing simulation without chromophore? Chromophore is important
>> in GFP. If you want i can send you the
phore. So, planarity
> does not matter to be ..
>
>
>
> On Thu, Jun 23, 2011 at 2:23 PM, Ramachandran G wrote:
>
>> Hi Bharat,
>> I used Amber force field, but still i am not statisfied with the
>> parameters which i used because after some nanosecond simulation(1 -2
Hi Bharat,
I used Amber force field, but still i am not statisfied with the
parameters which i used because after some nanosecond simulation(1 -2 ns)
the planarity of the sturcture changes. I tired changing the force constant
but still not much successfull. If you got success please let me know
Hi gmx-users.
I am doing MD simulation with the green fluorescent protein, where
confined water molecules exist inside the protein barrel.
During the coarse of the simulation i noticed these confined water molecule
get exchange with outside bulk water.
Is it possible to monitor or mark the wat
Hi gmx-users:
Is it possible to recover the topology from cpt file, it is so.. how
and what command i need to use?
Thanks
Rama
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Hello gmx users:
I did 1ns simulation for my system and have the trajectory and energy
files.
Now i want to see the energy of some specific residues. So, i
decompose(separated) the energy groups and edited the mdp file.
Using the mdp file, i created a new tpr file and rerun the mdrun using th
ore that is covalently bound to the protein
> backbone
> via a thiol-ester cysteine linkage Cys-69"...
>
> Maybe you forgot to specify a covalent bond in your topology...
>
> On 2011-04-20 06:46:54PM -0500, Ramachandran G wrote:
> > Hi gromacs users,
&
Hi gromacs users,
I am working on Photo active yellow protein.
Although i successfully build the force field and patched the
chromophore to the protein.
After energy minimizing the protein, the chromophore flies away separately.
I don't know whether i am missing anything?
Please help.
Ram
Hi gmx-users,
Is there is any software available to view the vibrational modes
selectively for particular wave number from the trajectory file.
Thanks and regards,
Rama
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Hi Mark, Justin,
Thanks for your help.
The details are helpful to improve my MD simulation. Also i need update my
gromacs version from 4.5.1 to 4.5.3.
Thanks again,
Rama
On Thu, Jan 13, 2011 at 3:47 PM, Justin A. Lemkul wrote:
>
>
> Ramachandran G wrote:
>
>> tha
= 0.5
;compressibility = 4.5e-05
;ref_p = 1.0
;Generate velocities is on at 300
gen_vel = no ; generate initial velocities
;gen_temp= 300.0 ; initial temperature
;gen_seed= 173529; random seeD
Please help.
thank you,
Rama
On Wed, Jan 12, 201
Hi gmx-users,
I tried extending one of simulation with modified mdp option.
First i used the command,
> grompp -f new.mdp -c old.tpr -o new.tpr
then i used the command to extend
> tpbconv -s new.tpr -extend timetoextendby -o next.tpr
Then,
> mdrun -s next.tpr -cpi previous.cpt
I surprised to
Hi Gromacs users,
I used g_mindist to calculate the minimum distance between a residue and
a group of water molecules.
Since distance is a length between two points in space, for the program
considers the bunch of water molecules(15 number)
what specific point does the group consider ? Thank yo
sion. Use something like:
>
> grompp -f md_extension.mdp -c MD_01.gro -n system.ndx -p system.top -t
> MD_01.trr -r MD_01.edr -o MD_02.tpr
>
> Itamar
>
> On 14/12/10 1:29 PM, Ramachandran G wrote:
>>
>> Hi gmx-users:
>> I am trying to extend my simulation run bu
Itamar
>
> On 14/12/10 1:29 PM, Ramachandran G wrote:
>>
>> Hi gmx-users:
>> I am trying to extend my simulation run but unfortunately i
>> deleted the file md.log. Is there any way i get my md.log file using
>> the existing .edr or .trr files so that i can pr
Hi gmx-users:
I am trying to extend my simulation run but unfortunately i
deleted the file md.log. Is there any way i get my md.log file using
the existing .edr or .trr files so that i can proceed further.
Thank you.
Rama
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Thank you,
Yes, i did energy minimization to the chromophore alone and it stays
stable
The problem arise when i do the energy minimization to the
GFP-chromophore full system.
It clearly shows the atoms which is expected to connect the
negihbouring residues is flying apart.
I am still checkin
27;t know where i am making
mistakes.
Should i need to give information in the Termini database flie *.tdb ? or
Is this due to wrong force constant values? or
Is my force field parameter has mistakes?
Thank your for you help.
Rama
On Fri, Nov 12, 2010 at 6:20 PM, Justin A. Lemkul wrote:
>
ustin A. Lemkul wrote:
>
>
> Ramachandran G wrote:
>>
>> Dear gromacs users:
>>
>> I have constructed the Amber03 force fields parameters
>> (bonds,angles, proper and imporer dihedral.) for the chromophore
>> (p-hydroxybenzylidene-imidazolino
22 PM, Justin A. Lemkul wrote:
>
>
> Ramachandran G wrote:
>>
>> Dear gromacs users:
>>
>> I have constructed the Amber03 force fields parameters
>> (bonds,angles, proper and imporer dihedral.) for the chromophore
>> (p-hydroxybenzylidene-imidazolino
Dear gromacs users:
I have constructed the Amber03 force fields parameters
(bonds,angles, proper and imporer dihedral.) for the chromophore
(p-hydroxybenzylidene-imidazolinone) inside GFP system and got the
topology. But after energy minimization of the system, the
conformation of the
; You can convert the .trr file to readable .gro/.g96 with trjconv.
> Frames with positive times will correspond to eigenvectors; the time
> indicates the eigenvector index. Make sure not to use any options like
> pbc/fitting :p
>
> Cheers,
>
> Tsjerk
>
> On Sat, Oct 16, 20
; indicates the eigenvector index. Make sure not to use any options like
> pbc/fitting :p
>
> Cheers,
>
> Tsjerk
>
> On Sat, Oct 16, 2010 at 7:00 AM, Ramachandran G wrote:
> > Hi,
> > Can anyone help to get the eigen vector in ascii format. I have with me
> the
&
in getting the ascii(readable) format of eigenvector and
hessian.mtx .
Your help is highly appreciated. Thank you.
with regards,
Rama
On Fri, Oct 15, 2010 at 2:29 PM, Ramachandran G wrote:
> Hi gmx users:
> I did normal mode analysis and got the hessian.mtx . Using the command
> g_n
Hi gmx users:
I did normal mode analysis and got the hessian.mtx . Using the command
g_nmeig_d on the hessian.mtx
i got the eigenfreq.xvg, eigenval.xvg, eigenvec.trr.
I need the complete eigenvector in the readable format. How i can get it?
Thank you.
with regards,
Rama
--
Postdoctoral Rese
Hi Justin,
Presently i too facing the same exact problem. I built the topology for
a chromophore in the protein and entered all the new parameters in the .rtp,
atp, hdb and defined the bonded and nonbonded parameters. Finally i got the
following error.
Fatal error:
Atom OXT in residue CRIH 64
Thank you for your clarification.
Rama
On Fri, Sep 17, 2010 at 5:49 PM, Justin A. Lemkul wrote:
>
>
> Ramachandran G wrote:
>
>> Thank you Justin,
>> You are right i am not comparing the same force field.
>> But i am still curious to know the conversion fact
PM, Justin A. Lemkul wrote:
>
>
> Ramachandran G wrote:
>
>> I understood from the gromacs manual the units for epsilon and sigma are
>> KJ/mol and nm and the corresponding units in MOIL Kcal/mol and Angstom. But
>> when i checked for some atoms, the epsilon values
PM, Justin A. Lemkul wrote:
>
>
> Ramachandran G wrote:
>
>> Hi gmx-users,
>>I would like to know the units conversion of epsilon, sigma (from
>> non-bonded, Van der Waal interaction) from Charmm or MOIL to gromacs.
>> Thank you.
>>
>>
> My
Hi gmx-users,
I would like to know the units conversion of epsilon, sigma (from
non-bonded, Van der Waal interaction) from Charmm or MOIL to gromacs.
Thank you.
with regards,
Rama
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Dear gmx-users:
I am trying to get the topology for a chromophore exist in the Green
fluoresent protein. Although to some extent i got success in building the
parameters in the 'ff*.rtp' file,
i got struck in building 'atom type parameter' ( ff*.atp). I am trying to
use Charmm force field.
Hi gmx users,
Since i wanted to use 'TIP5P' water model along with charmm forcefield,
i modified the 'tip5p.itp' file according to other existing force field in
gromacs
And i have made the following changes in the 'ffcharmm27_ffnb.itp'
#ifdef HEAVY_H
OWT58 9.9514000.0
.
Your help will be highly appreciated. Thank you.
Yours sincerely,
Rama
On Wed, Jun 30, 2010 at 8:30 PM, Mark Abraham wrote:
>
>
> - Original Message -
> From: Ramachandran G
> Date: Thursday, July 1, 2010 11:42
> Subject: [gmx-users] amber/charmm force field and
Hi gromacs users:
Using amber/charmm force field we simulated a solvated protein system
at different temperature(300,250 and 200K).
I used TIP5P water model and applied NVT ensemble . We analyzed the hydrogen
bond life time correlation function(HBCF) to study the protein water
interactions. At
Dear gromacs users,
I could not able to use tip5p water model with charmm force field.
If anybody tried successfully, please help me.
Thank you.
with regards,
Rama
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Hello gromacs users:
I installed the new version of gromacs and tried to run 'mdrun_mpi'
in parrallel but it gives the error pasted below.
When i switched the constrain from 'shake' to 'lincs' it runs. I know
'shake' algorithm compilation was done but i don't why
i am getting this error.
> Hi,
>
> 15 apr 2010 kl. 11.11 skrev Ramachandran G:
>
> Hello Par:
>Using the latest git i could able to work on my oxy-hemoglobin
> system with new gromacs version 4.0.5 successfully.
>
> CHARMM is not supportd in version 4.0.5, you probably mean the developer
now added the charmm files to git head and the protein and lipid
> parts should work at least. Simply check out the latest git and the charmm
> parameters should show up in pdb2gmx.
>
> /Pär
>
> 11 mar 2010 kl. 03.04 skrev Ramachandran G:
>
> Hello Bjelkumar,
> Than
/03/2010 2:51 PM, Ramachandran G wrote:
>
>> Dear gromacs users:
>> I am using following mdp file as input for simulating the
>> system with NVE ensemble. But when i check the 'Total energy',
>> it doesn't seems to remain constant and keep decreasi
Dear gromacs users:
I am using following mdp file as input for simulating the system
with NVE ensemble. But when i check the 'Total energy',
it doesn't seems to remain constant and keep decreasing. I am also giving
some part of my output. Thanks for your help
Rama
title= W
Dear Mark and David,
Thanks you, i will check the paper very carefully and try again.
regards,
Rama
On Sat, Feb 27, 2010 at 1:13 AM, Mark Abraham wrote:
> On 27/02/2010 7:31 PM, Ramachandran G wrote:
>
>> Dear Dr. van der Spoel:
>>
>> Thanks for the clarification
t;g_hbond",
and/or is it possible to customize the t in gromacs?
best
Rama
On Fri, Feb 26, 2010 at 10:03 PM, David van der Spoel
wrote:
> On 2010-02-27 03.27, Ramachandran G wrote:
>
>> Hi gromacs users:
>> As you know autocorrelation function C(t)
>>
>&g
Hi gromacs users:
As you know autocorrelation function C(t)
C(t) =
't' value can start from 0 but, i would like to know what value does
gromacs use, more specifically for g_hbond.
Can anyone help me? Thank you.
Rama
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Dear gromacs users:
I am trying to use ffcharmm27 patched with gromacs, since it does
not have 'heme' i tried
add it manually but still i am getting error while doing pdb2gmx. If anybody
have already done 'HEME' protein using
charmm force field in gromacs, please help me. Thanks
Rama
--
Dear gromacs users:
I am trying to get the topology file for oxy-hemoglobin. As
suggested below in the link below, I am trying to modify my itp or rtp
file.
http://osdir.com/ml/science.biology.gromacs.user/2006-07/msg00236.html
But, if anybody has already constructed rtp file for oxy hem
Dear gromacs users:
I have a couple of questions:
While doing auto correlation function under what condition i need
to use polynomials?
Apart from the fit functions existing in the gromacs how can i use
different functions like
stretched exponential in the form P(t)=ex
Dear gmx users,
I have created a water box using tip5p model and trying to get the
topology file for that using
pdb2gmx but, i couldn't able to create the topology file and i got the error
message
Fatal error:
Atom OL1 in residue HO5 1 not found in rtp entry with 5 atoms
while
Thanks, it works when i give proper time.
Previously i made mistake by giving the time frame number.
Rama
On Thu, Dec 10, 2009 at 9:13 PM, Justin A. Lemkul wrote:
>
>
> Ramachandran G wrote:
>
>> Thanks for your help.
>> I have tried the command
>>
>> trjc
, Justin A. Lemkul wrote:
>
>
> Ramachandran G wrote:
>
>> Dear gromacs users:
>> Can any one tell me how can i split a trajectory file from a
>> specific time interval of my interest.
>> For example if i have a trajectory file up to 0-100ps, and my int
Dear gromacs users:
Can any one tell me how can i split a trajectory file from a
specific time interval of my interest.
For example if i have a trajectory file up to 0-100ps, and my interest is to
consider part of the trajectory from 50-75ps,
how i can go about it either by splitting the t
Hi all,
I am trying to do velocity auto-correlation function(VACF) for the
'oxygen atom' present in a 63 Ang. cubic water box, simulated upto 500ps.
And the velocities are stored at every 5fs. While doing the
analysis(g_velacc), it got struck at 400ps, since if felt it is mainly due
to the mem
Dear all,
I am trying to minimize a protein structure but i noticed initially
before it starts minimization, it gives warning
-
Warning: 1-4 interaction between 1434 and 1490 at distance 1.783 which is
larger than the 1-4 table size 1.000 nm
These are ignor
Dear all,
It is known that force field for the heme group doesn't exist
in gromacs. So i tried to use amber force fields(AMBER94, AMBER99,
AMBER99p, AMBER03, AMBERGS, AMBERGSs) by patching with my latest
gromacs version 4.0.5 but still it gives the error message
'Residue 'HEME' not found in
while(read_next_x(status,&t,natoms,x,box)); */
} while(read_next_frame(status,&fr));
close_trj(status);
if (out != -1)
close_trx(out);
if (fp)
ffclose(fp);
thanx(stderr);
return 0;
}
On Mon, Nov 2, 2009 at 9:41 PM, Mark Abraham wrote:
> Ramachandran G wrote:
version.
Thanks.
Rama
On Mon, Nov 2, 2009 at 6:36 PM, Mark Abraham wrote:
> Ramachandran G wrote:
>>
>> Thank you, I have installed new version of gromacs4.0.5 and trjorder
>> works fine in giving me the trajectory file(ordered.trr) but using
>> this file when i try
cs? Thank you again.
Regards,
Rama
On Sat, Oct 31, 2009 at 11:43 PM, David van der Spoel
wrote:
> Ramachandran G wrote:
>>
>> Dear David,
>> Thank you for you help. It is very much helpful for me.
>>
>> I have one more question. Is it possible to create index file
:43 AM, David van der Spoel
wrote:
> Ramachandran G wrote:
>>
>> Dear David,
>> Thank you for you help. It is very much helpful for me.
>>
>> I have one more question. Is it possible to create index file for the
>> oxygen atom or water molecules alone e
:
> Ramachandran G wrote:
>>
>> I have used the option as follows:
>> g_hbond -f file.trr -s file.tpr -n file.ndx -ac output.xvg
>
> -life koko.xvg
>
>>
>> To find the continious HB-correlation function, what option should i
>> need to use.
>> Than
I have used the option as follows:
g_hbond -f file.trr -s file.tpr -n file.ndx -ac output.xvg
To find the continious HB-correlation function, what option should i
need to use.
Thank you for your help.
Rama
On Tue, Oct 6, 2009 at 11:40 PM, David van der Spoel
wrote:
> Ramachandran G wr
you please help me to understand thank you.
Rama
On Tue, Oct 6, 2009 at 3:06 AM, David van der Spoel
wrote:
> Ramachandran G wrote:
>>
>> C_HB(T) = /
>>
>> S_HB(T) = /
>>
>>
>> h(T) =
the C_HB(t). But i am not very sure
about that. Anybody knows
please help me. Thank you.
Rama
On Tue, Oct 6, 2009 at 2:37 AM, David van der Spoel
wrote:
> Ramachandran G wrote:
>>
>> Dear gromacs users:
>> I like to know whether gromacs will calculate S-type hydroge
Dear gromacs users:
I like to know whether gromacs will calculate S-type hydrogen
bond correlation function?
If it so how it can be done? Thank you.
Rama
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