Hi all,
How can I convert 3 different gromacs itp file to generate single psf file
?
Is there any command to do that
I tried using top2psf.pl script to do that , but it failed.
Thank you.
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dear users,
I am encountering a problem with script, the summary.dat file does
not generate
any value. But if I run the distance command one at the time , it is
generating the value, I could not figure out where I am goingperlgmx wrong.
can anyone tell where lies the mistake?mistake?
Thank you
only tool you own is a hammer, every problem begins to resemble a
> nail.
>
>
> On 17 October 2017 at 21:16, Kingsley Theras Primus Dass .
> <105726...@gms.tcu.edu.tw> wrote:
> > Hi all,
> > I have a very basic question about essential dynamics. I want to know
> >
Hi all,
I have a very basic question about essential dynamics. I want to know
whether essential dynamics function is similar to Accelerated MD ? Or
essential dynamics is different from Accelerated MD ?
Thanks in advance.
Kingsleg Theras
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Dear all,
I am trying umbrella sampling. when I gmx wham command I get the following
error. I checked my tpr.dat and px.dat files, everything seems to be okay.
but still, i get this error. can you suggest some solutions?
Found 22 tpr and 22 pull position files in tpr.dat and px.dat, respec
ine here?
> we can judge where you are wrong
>
>
> On Aug 9, 2017 12:50 PM, "Kingsley Theras Primus Dass ." <
> 105726...@gms.tcu.edu.tw> wrote:
>
> Hi everyone,
>
> I am trying to calculate the binding free energy between protein and ligand
> by using MM/P
Hi everyone,
I am trying to calculate the binding free energy between protein and ligand
by using MM/PBSA. I included all the .itp files. But when run the command,
am getting an error saying "NO XTC" Could someone help me, what would be
wrong, why such error occurs. i have pasted the error messag
Hii
I am trying out the umbrella sampling tutorial. I finished generating a
series of coordinate file , but when i run the perl script the
summary_distance.dat doesnt generate the COM distance value
What would be the possible reason for this ?
Thank you
Kingsley
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2017 9:31 p.m., "RAHUL SURESH" wrote:
I am not sure but I think u can calculate t along with rmsf calculation
where you have to generate additional output as pdb file.
On Tue, 9 May 2017 at 6:58 PM, Kingsley Theras Primus Dass . <
105726...@gms.tcu.edu.tw> wrote:
> Hi ever
Hi everyone !
I want to calculate b-factor , but I don't kno how to calculate. Can
anyone please tell me how to calculate b-factor for a protein and how to
analyse it ...
Thanks in advance
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Hi,
I tried to calculate binding free energy for my protein. I tried using MM
/ PBSA, when i ran the program i am getting an error. Could you please say
why such error is occuring and how should i need to rectify it.
the error message is below
17:54:41
The directory RUN_ is not present. Plea
-- Forwarded message --
From: Kingsley Theras Primus Dass . <105726...@gms.tcu.edu.tw>
Date: 2017-02-23 18:06 GMT+08:00
Subject: error in minimization
To: gromacs.org_gmx-users@maillist.sys.kth.se, gmx-us...@gromacs.org
Hello !!
I am encountering an error in minimizatio
Hello !!
I am encountering an error in minimization step. Help me out to avoid this
kind of error.
The error message says,
WARNING: Listed nonbonded interaction between particles 2999 and 3006
At distance 2.442 which is larger than the table limit 2.400 nm.
This is capable capable any
A doubt
Hello !!
I am encountering an error in minimization step. Help me out to avoid this
kind of error.
The error message says,
WARNING: Listed nonbonded interaction between particles 2999 and 3006
At distance 2.442 which is larger than the table limit 2.400 nm.
This is capable capable any
A doubt
Dear Users!!
I have a question about RMSD. I ran MＤ simulaton for 500ns and connected
all my .xtc files using trjcat command.
And , then I used g_rms command with the connected .xtc file to calculate
RMSD for backbone atoms. But , when I run g_rms command , I get a warning
as follows:
WARNIN
Even when I add the new atom types to aminoacid.rtp, .hdb , .atp ,
Still it shows the same error
Could you please suggest some solutions.
Thank you in advance
On 8 Nov 2016 6:59 p.m., "Justin Lemkul" wrote:
>
>
> On 11/7/16 10:44 PM, Kingsley Theras Primus Dass
Hello users!!
I generated a Topology file for SO3- using ATB topology generator , which
is compatible with GROMACS. Then I copied the .rtp file from ATB and pasted
it into GROMACS aminoacid.rtp.
The partial charge of aminoacid sulfated-tyrosine was -1.
When I run -pdb2gmx there was error sayin
-- Forwarded message --
From: "Kingsley Theras Primus Dass ." <105726...@gms.tcu.edu.tw>
Date: 3 Nov 2016 11:42 a.m.
Subject: [gmx-users] (no subject)
To:
Cc:
Hello users !
I want to Add SO3- to tyrosine residue of my protein. I generated the
topology fi
Hello users !
I want to Add SO3- to tyrosine residue of my protein. I generated the
topology file for SO3- (TYS) residue using PRODRUG server and incorporated
that topology into my topology. I am using GROMACS45a3 force field . but
still when i try running pdb2gmx , it shows error.
could you ple
Hello !
As I am new to this field , I have some doubts . I want to sulfate the
tyrosine residue in the chemokine receptor ...
But wen I download a pdb file that has sulfated tyrosine residue and run
pdb2gmx command in GROMACS ,it is showing a error message ...how can i come
over this problem
Progr
hello !
I want know to how to sulfate the tyrosine residue in GROMACS? when i try
to sulfate , GROMACS is showing error saying that it is not in the .rtp
file. Kindly, help me with it .
thank you
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