iated. Thanks a
ton!
Sharada
"The person addressed in the email is the sole authorized recipient.
Should you receive it in error, immediately notify the sender of the
error and delete the e-mail. Any unauthorized dissemination or copying
of this e-mail (or any attachment to this e-m
Uday,
You are reproducing the output of md.csh. I would also like to see the
contents of md.csh to know the gromacs commands therein. This would help to see
where the error is coming. Please paste the file md.csh.
sharada
Dear Uday,
What is the command you have given ? Please paste the command lines.
sharada
-- Original Message --
From: udaya kiran
To: gmx-users@gromacs.org
Date: Mon, 13 Dec 2010 17:22:07 +0100
Subject: [gmx-users] ERROR: Source code file: statutil.c, line: 727
Dear All,
I am unable to carry out
Hi,
You need to specify the input file with -f flag and -i is for the itp file
which is the output and that is any way created by default. Just remove -i from
the command and it will work.
best,
sharada
-- Original Message --
From: Asmaa Elsheshiny
To: "gmx-users@gromacs.org"
Date:
Hi,
Use splitat for group 3.
sharada
-- Original Message --
From: Venkat Reddy
To: Discussion list for GROMACS users
Date: Thu, 9 Jul 2009 19:54:18 +0530
Subject: Re: [gmx-users] make_ndx option
Hi Anirban !
First u hav to notedown the C-alpha atoms nos seperately from ur atom file.
Then
hello,
I have downloaded the tar file from the github and extracted the contents.
However I am unable to understand the README file as it is in a language other
than english. Could you kindly provide the instructions how to go about using
it.
thanks for the help
sharada
-- Original Message
Hi,
I waited for it to finish for almost 5 days nothing happened except creation
of those files. I had posted a similar mail some time back. Is there no
solution for this. Is it something to do with speed of the system? I ran the
program on HP dual core system.
sharada
-- Original
Do you intend to protonate a pair of cysteins and not make a SS bond?
Then pdb2gmx -ss should do the job.
Sharada
-- Original Message --
From: sharada
To: Discussion list for GROMACS users
Date: Fri, 6 Mar 2009 12:28:54 +0530 (IST)
Subject: Re: Re: [gmx-users] How to break a disulfide bond
If you donot make it, it is as good as breaking it...
Sharada
-- Original Message --
From: Venkat Reddy
To: Discussion list for GROMACS users
Date: Fri, 6 Mar 2009 11:31:57 +0530
Subject: Re: [gmx-users] How to break a disulfide bond ???
Hai !
with "pdb2gmx -ss", i can select the ss
pdb2gmx -h
sharada
-- Original Message --
From: Venkat Reddy
To: Discussion list for GROMACS users
Date: Fri, 6 Mar 2009 10:50:24 +0530
Subject: [gmx-users] How to break a disulfide bond ???
Hai Every one ! Is it possible to break a disulfide bridge using gromacs
?If so,Can anybody suggest
9 6.9) to the ones as shown below.
Kindly guide me through.
Regards
sharada
# ==>
< A V E R A G E S >
<== ### ==>
Current ref_t for group Protein:300.0
Current ref_t for group Other:300.0
Energies (kJ/mol)
Angle G9
Dear Nuno Azoia,
I followed one of the replies given at gmx-users list which I quote here...I
donot know whether this is right ? In that case the temperature has truly
changed from 0 to 60 how is it possible if Tcoupl = no...?I am in doubt.
Kindly comment.
sharada
Re: [gmx-users] how to write
Dear gromacs-users,
I am heating a peptidein methanol from 0K - 300K. The simulated annealing
protocol is given in the md.mdp file shown below:
title = cpeptide MD
cpp = /lib/cpp
constraints = all-bonds
in
of rvdw, rcoulomb & rlist ? In that
case what would be the set of values if I am working with 45a3 forcefield with
PME option ? How do I give correction term for dispersion otherwise? Are the
methanol .gro and itp files that I am taking the right ones ?
regards,
sharada
-- Original Message
to a change in the
simulation or this value holds good only if reaction field is on ?
sharada
-- Original Message --
From: "Justin A. Lemkul"
To: Discussion list for GROMACS users
Date: Sat, 31 Jan 2009 00:42:36 -0500
Subject: Re: [gmx-users] Melittin in methanol...
sharada wrote:
>
methanol.
Thanks..
sharada
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methanol.
Thanks..
sharada
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376560.
2 3 10.1 313800.
[ angles ]
; aiajak funct c0 c1
1 2 3 1 108.53 397.5
I would try using the new force field.
sharada
-- Original Message --
From: "Justin A. Lemkul"
To: Discussion list for GROMACS users
Date: Thu, 29 J
water like this but not in methanol. Can any
one tell me where I am going wrong. Any insight in this direction is welcome.
Thankyou in advance
sharada
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e and make install but it does not
compile/install. How should I install it ? Thankyou for the time.
sharada
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I tried to install it seperately using make and make install but it does not
compile/install. How should I install it ? Thankyou for the time.
sharada
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e he has considered the angle to be greater than or equal to
135 and the HB distance as smaller than .25nm. Yes the program has the
provision to vary these values. Thank you for the clarifications.
have a good day.
sharada
-- Original Message --
From: David van der Spoel <[EMAIL PROTECT
degrees and cut-off radius .35 nm mean in the program
g_hbond. Is it considering the hydrogen bond angle of 120 +/- 30 ? In that case
cut-off angle 60 & 120 in other versions does not make sense ... Kindly clarify
my doubts
regards
sharada
-- Original Message --
From: "Anil Kumar" <
dear gmx-users,
I have a very fundamental query. I am trying to obtain the backbone hydrogen
bonds formed during a 15ns simulation of a 35 long protein. When I do this by
using g_hbond and selecting the Backbone groups, I am getting no hydrogen bonds
at all . However, when I plot the hydrogen bo
Chandrika,
Did you try using the -settime option ?
sharada (CCMB)
-- Original Message --
From: CHANDRIKA RAO <[EMAIL PROTECTED]>
To: gmx-users@gromacs.org
Date: Fri, 29 Feb 2008 11:10:47 +0530
Subject: [gmx-users] Merge two trajectories
Dear All,
We have c
Hi candrika,
Using the trjcat program with -settime option. Try typing trjcat -h to get help.
sharada
CCMB
-- Original Message --
From: CHANDRIKA RAO <[EMAIL PROTECTED]>
To: gmx-users@gromacs.org
Date: Fri, 29 Feb 2008 11:10:47 +0530
Subject: [gmx-users] Mer
) = 1.0e+01
Number of steps= 2000
Going to use C-settle (1108 waters)
wo = 0.33, wh =0.33, wohh = 3, rc = 0.08165, ra = 0.0384897
rb = 0.0192449, rc2 = 0.1633, rone = 1, dHH = 0.1633, dOH = 0.1
Grid: 4 x 5 x 4 cells}
regards
sharada
-- Original Message --
From: "Xavier Pe
to energy minimize the system which
what I am trying to do ! What is this ci value and why is it so high? Kindly
help me I am once again stuck.
regards
sharada
-- Original Message --
From: "Xavier Periole" <[EMAIL PROTECTED]>
To: Discussion list for GROMACS users
Date: Tue, 11 D
ol.itp and methanol216.gro which could be possible
only through root.
regards
sharada
methanol.itp
D
ROMOS96
1 CMET 1 MeOHMe1 10.176 15.035
2 OMET 1 MeOHO21 -0.574 15.999
3 H1 MeOHH3 10.398 1.008
#else
1 CMET 1 MeOHMe1 1 Regards
sharada 0.29 15.035
2
O2 1636 2.457 3.218 2.567
528MeOHH3 1637 2.390 3.204 2.494
3.30500 3.58500 2.95900
Why does it say there are no SOL molecules. Where exactly am I going wrong ?
Kindly advice me. Thankyou for your patience.
sharada
___
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any idea how much space does it occupy ? ( I am hard of Disk
space) . Pray for me.
regards
sharada
-- Original Message --
From: Martin =?iso-8859-1?q?H=F6fling?= <[EMAIL PROTECTED]>
To: Discussion list for GROMACS users
Date: Wed, 17 Jan 2007 13:51:33 +0100
Subject: Re: [gmx-users] Error
correct by retyping again those lines. I have
posted a mail before this. Hope you get your Doctorate soon !!.
Regards
sharada
-- Original Message --
From: Martin =?utf-8?q?H=C3=B6fling?= <[EMAIL PROTECTED]>
To: Discussion list for GROMACS users
Date: Wed, 17 Jan 2007 10:55:26 +0100
Subje
got solved or not ? I would like to request him to give me some suggestions in
this regard. I am desperate in installing it on SGI using MIPSpro compilers
(cc) before I switch over to gcc as this would take time.
Thanks in advance
Sharada
-- Original Message --
From: sharada <[EMAIL PROTECTED]&
hat
if these are corrected then may be my compilation would go smoothly, however I
donot know where is the 'main.c' program. If I am right then I would like to do
this first, if you can tell me where to look for main.c or is it possible ?
with regards
sharada
"
-- O
let me know
so that my problem is solved. gcc compilers are not loaded on the Octane system
otherwise I would have tried installing the package with it. My previous mail
got cut and it was sent half way sorry about the repetition..
with regards
sharada
-- Original Message --
From: sharada <[EM
007 13:39 schrieb sharada:
> I am using the MIPSpro Compilers Version 7.3 . Is there a problem with that
> version ? I had installed the Gromacs version 3.01 and version 3.2 using
> the same compilers earlier there was no problem why now.? Thanks for
> the reply
I was thinking about
I am using the MIPSpro Compilers Version 7.3 . Is there a problem with that
version ? I had installed the Gromacs version 3.01 and version 3.2 using the
same compilers earlier there was no problem why now.?
Thanks for the reply
regards
sharada
-- Original
Dear Gromacs users,
I am installing the Gromacs version 3.3.1 on the SGI Octane with IRIX 6.5 R12000
system. I could successfully installed fftw package and trying the compile
gromacs.
I am getting the following at the end of the 'make' command :
These are the last few lines after the mak
Swamy Kakumani,
Thank you for the reply. I am not working on the parallel machines, Linux
version is Fedora Core 4 System's configuration is listed below in my previous
mail.
regards
sharada
-- Original Message --
From: swamy kakumani <[EMAIL PROTEC
over write.
Can I keep both the versions loaded on the system or will there be a clash ?
Do I have to load fftw once again ?
Bothering you with too many questions ! Answers for these would help me to
decide .
Thanks in advance.
sharada
-- Original Message --
From: "Mark Abraham" <[EM
) what may be the
reason ?
Thanks for the patience ...
regards
A .Sharada Devi
Technical Officer C
Center for Cellular Molecular
Biology
Habsiguda Uppal Road
Hyderabad -57
India
-- Original Message --
From: Caterina Arcangeli <[EMAIL PROTECTED]>
To: Discussion list for GROMACS users
help
regards
sharada
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Can't post?
the pdb2gmx program is checking for
S-S distance to less than or equal to 2A and makes the bond . Am I right
? Is there a way out in this direction. Kindly help or any other
suggestion is welcome. Anticipating for a reply.
Regards,
sharada
Mark Abraham wrote:
sharada wrote:
Hello gromacs
cysteins to form disulphide bonds ? I am
sure there must be a way . Any suggestions or ideas. Thanks a ton in
advance.
sharada
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sharada
Mark Abraham wrote:
sharada wrote:
Hello Erik,
Thank you for suggesting the idea. I have got the required help from
FFTW authors. I could load the Gromacs successfully. I have even done
a test run (pdb2gmx - mdrun) on my protein in water. However I am
unable to finally visualise the
says command not found. Why is it giving me this error when all the
other programs are working ? I could't locate the link for this program
in any folder. Where is it installed ? My configure,make,make install
and make links didnot give any errors ! Kindly guide me. Thanks in
advance.
sh
Hi gromacs users,I am trying to install gromacs on Linux. While installing the fftw module , I am getting the following errorat the ./configure stage:[EMAIL PROTECTED] fftw-3.1.2]# ./configure --enable-float --enable-threads --enable-ssechecking for a BSD-
Hi gromacs users,I am trying to install gromacs on Linux. While installing the fftw module , I am getting the following errorat the ./configure stage:[EMAIL PROTECTED] fftw-3.1.2]# ./configure --enable-float --enable-threads --enable-ssechecking for a BSD-compatible install... /usr/bin/install -c
? anything to do with my system that
PME does not support ? the programs just hang for a long time.
Mark Abraham wrote:
sharada wrote:
Dear Dr. Tsjerk Wassenaar,
Thanks for replying . The force field I am using is ffG43a1.itp in
Gromacs 3.1.4 version and I tried all combinations CL,CL- Cl
Dear Dr. Tsjerk Wassenaar,
Thanks for replying . The force field I am using is ffG43a1.itp in
Gromacs 3.1.4 version and I tried all combinations CL,CL- Cl - cl etc
sharada
Tsjerk Wassenaar wrote:
Hi Sharada,
The name depends on the force field used (you didn't mention). You may
luding 3 bonded neighbours for Protein_B 1
Excluding 2 bonded neighbours for SOL 1366
Cleaning up temporary file grompp013645
Fatal error: No such moleculetype Cl
Where am I going wrong I am not able to figure out. Has anybody come
across such problem...please
quot;pdb2gmx:Command not found. " what could be the>problem?>Suggest me a solution.>>>regards,>>sharada >>A.sharada Devi>Center for Cellular and molecular Biology>Uppal Road>Hyderabad -500 007>AP>INDIA>>>>>__
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