rc/gmxlib/cyggmx_d-8.dll' is not able to
locate it.
Please help me
shahid Nayeem
On Wed, Sep 11, 2013 at 1:02 PM, shahid nayeem wrote:
> Thanks. But when I ran make again I am getting this error
> [ 0%] Built target gmxfftw
> make[2]: *** No rule to make target
> `//cygdri
recipe for target
`src/gmxlib/CMakeFiles/gmx.dir/all' failed
make[1]: *** [src/gmxlib/CMakeFiles/gmx.dir/all] Error 2
Makefile:146: recipe for target `all' failed
make: *** [all] Error 2
shahid Nayeem
On Wed, Sep 11, 2013 at 12:39 PM, Mark Abraham wrote:
> For technical reas
ll' failed
make: *** [all] Error 2
Please help me to compile gromacs 4.6.3 on cygwin
Shahid Nayeem
On Tue, Sep 10, 2013 at 9:13 PM, Mirco Wahab <
mirco.wa...@chemie.tu-freiberg.de> wrote:
> On 10.09.2013 08:20, shahid nayeem wrote:
>
>> I am installing gromacs -4.6.3 on cygwi
Dear all
I am installing gromacs -4.6.3 on cygwin with following commands
tar -xvzf gramcs-4.6.3.tar.gz
cd gromacs-4.6.3
mkdir build
cd build
cmake .. -DGMX_BUILD_OWN_FFTW=ON -DGMX_DOUBLE=on
It runs fine and write file in build directory.
when I run make command it gives following error.
[ 15%] B
Dear all
I am installing gromacs -4.6.3 on cygwin with following commands
tar -xvzf gramcs-4.6.3.tar.gz
cd gromacs-4.6.3
mkdir build
cd build
cmake .. -DGMX_BUILD_OWN_FFTW=ON -DGMX_DOUBLE=on
It runs fine and write file in build directory.
when I run make command it gives following error.
[ 15%] B
nges.
> What is your system? A peptide? A globular protein?
>
> Best,
> Jesper
>
> On May 3, 2013, at 7:33 PM, shahid nayeem wrote:
>
> > Thanks a lot Erik and Baptista
> > I am interested in simulating the change in secondary structure which is
> > supposed to be
of the time... :)
>
> Best,
> Antonio
>
>
> On Fri, 3 May 2013, Erik Marklund wrote:
>
> Yes that's what lambda dynamics does. I mentioned it since it addresses
>> the interplay between protonation and structure. So to answer your original
>> question: it dep
uld check out
> the papers on lambda dynamics by C. Brooks III for an interesting take on
> sampling multiple protonation states.
>
> Best,
>
> Erik
>
> On 3 May 2013, at 14:05, shahid nayeem wrote:
>
> > Thanks a lot Erik. Could I get some reference based on
ce, will be horribly wrong without dynamic protonation. Much (but not
> all) structural biology, however, will be largely unaffected.
>
> Erik
>
> On 3 May 2013, at 04:30, shahid nayeem wrote:
>
> > Dear all
> >
> > Can someone enlighten me on the reliability of the
Dear all
Can someone enlighten me on the reliability of the results obtained from
constant protonation state (assigned by different pKa value at different
pH) MD simulation. Also want to know its reliability in case of implicit
solvation model such as PB/GB calculation.
Shahid
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se are good for analysis!
>
> Francesco
>
>
> 2013/3/19 shahid nayeem
>
>> Thanks Francesco.
>> But my problem is exactly opposite. I do have a .top file containing
>> both chain linked by disulfide bridge. I ran the simulation. Now I
>> have extracted .xtc file for ea
gmx
> with the option -chainsep ter. The result is supposed to be a topology
> where your chain are grouped in
> a single molecule,making possible to create the bridge, and at the same
> time you keep the chain name
> for future analysis.
>
> Francesco
>
>
> 2013/3/19 sha
make my .xtc and .top file compatible.
Shahid
On Tue, Mar 19, 2013 at 2:07 AM, Justin Lemkul wrote:
>
>
> On 3/18/13 12:35 PM, shahid nayeem wrote:
>>
>> Hi
>> Is it possible to write .top file from .xtc and .tpr using index.ndx
>> so that .top is available for t
I am using Gromacs-4.5.4 and this does not have -cys option in pdb2gmx.
shahid
On Tue, Mar 19, 2013 at 2:06 AM, Justin Lemkul wrote:
>
>
> On 3/18/13 10:39 AM, shahid nayeem wrote:
>>
>> Hi All
>> How can I get a topology file using pdb2gmx from a single chain
>
Hi All
How can I get a topology file using pdb2gmx from a single chain
polypeptide with one of the CYS, SH in the form of SG as if it is
involved in disulfide linkage, while the other chain with which I
expect it to form disulfide link is not in the input pdb file. or can
I use pdb2gmx command and
Hi Justin
If I use the boundwaters.ndx to write another .ndx file using 1 & 2 &
3 & 4 and so on over all snapshots then also I should get the common
water molecules in these snapshots. Am I right.
Shahid
On Mon, Jan 28, 2013 at 9:03 PM, Justin Lemkul wrote:
>
>
> On 1/2
this protein and get the pdb of protein with inserted
peptide segment.
shahid Nayeem
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Dear all
Please suggest me a tool with which I can generate insertion mutants
from a .pdb file. I want to insert new 10-15 aa sequence of AA in
between an existing .pdb file. The tool should write a new .pdb file
with altered coordinates after insertion of new sequence and
minimization of the stru
I want to simulate without building the missing residue. Does gromacs
have an option of capping. I am using Gromacs 4.5.4. If not then
suggest some software which I may use.
Shahid nayeem
On Fri, Aug 17, 2012 at 10:03 AM, Mark Abraham wrote:
> On 17/08/2012 2:28 PM, shahid nayeem wr
computationally more expensive. Will these results
will be O.K.
Shahid Nayeem
On Fri, Aug 17, 2012 at 9:37 AM, Mark Abraham wrote:
> On 17/08/2012 2:02 PM, shahid nayeem wrote:
>>
>> Dear all
>>>
>>> One basic clarification. How does LINCS algorithm influences the re
Dear all
> One basic clarification. How does LINCS algorithm influences the results
> of final production run. In what respect a minimization, pr and final
> simulation done with constraints = none and with constraint= all_bonds are
> different.
> Shahid Nayeem
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Dear users
By mistake I have deleted my .tpr file after running simulation. Is it
possible to generate .tpr file from .xtc .gro .log and .ene file of final
production run.
shahid Nayeem
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Please
-nBootstrap 200 -bsres
bsResult_mut.xvg -bsprof bsprofile_mut.xvg -ac
I get the values exactly opposite to my expectation and unable to find out
where I am wrong please suggest.
Shahid Nayeem
On Thu, Mar 15, 2012 at 3:31 PM, shahid nayeem wrote:
> I have added some new windows in mutant umbre
http://www.freefilehosting.net/umbrellamut
On Wed, Mar 7, 2012 at 4:38 PM, Justin A. Lemkul wrote:
>
>
> shahid nayeem wrote:
>
>> The attached profile.xvg and histo.xvg are here.
>> sorry for sending earlier mail without attachments
>> Shahid Nayeem
>>
>&
for it. My profile.xvg and histo.xvg are right or they need more
improvement.
Shahid Nayeem
On Tue, Feb 28, 2012 at 7:44 PM, Justin A. Lemkul wrote:
>
>
> shahid nayeem wrote:
>
>> Thanks. But Does that mean that I should look in pullf.xvg of each window
>> and see whethe
Thanks. But Does that mean that I should look in pullf.xvg of each window
and see whether the value is converged or not. If not then I should extend
the simulation.
Shahid Nayeem
On Sat, Feb 25, 2012 at 12:05 AM, Justin A. Lemkul wrote:
>
>
> shahid nayeem wrote:
>
>>
simulation required in each window with this information.
Shahid nayeem
On Fri, Feb 24, 2012 at 7:56 PM, Justin A. Lemkul wrote:
>
>
> shahid nayeem wrote:
>
>> I thought this time to be sufficient without any reasonable basis.
>>
>
> If you pick an arbitrary t
I thought this time to be sufficient without any reasonable basis.
shahid Nayeem
On Fri, Feb 24, 2012 at 7:40 PM, Justin A. Lemkul wrote:
>
>
> shahid nayeem wrote:
>
>> My system is a protein-protein complex. After pulling I selected windows
>> at 0.1nm from an initia
equilibriation.
Shahid Nayeem
On Tue, Feb 21, 2012 at 6:42 PM, Justin A. Lemkul wrote:
>
>
> shahid nayeem wrote:
>
>> Initially I used g_wham -if pullf-files.dat -it tpr-files.dat -unit Kcal
>> -histo. But now as suggested by you I added -b 1000 -e 1 leaving 1ns
>&g
Initially I used g_wham -if pullf-files.dat -it tpr-files.dat -unit Kcal
-histo. But now as suggested by you I added -b 1000 -e 1 leaving 1ns
for equilibriation. The new profile.xvg is attached. How can I further
improve it.
Shahid Nayeem
On Tue, Feb 21, 2012 at 1:04 AM, Justin A. Lemkul
am not getting smooth convergence.
Shahid Nayeem
On Mon, Feb 20, 2012 at 10:48 PM, shahid nayeem wrote:
> I am attaching a profile.xvg and histo.xvg. In each window 10ns sampling
> was done. The umbrella pullcode used is as follows.
> ; Pull code
> pull= umbrella
you earlier.
shahid Nayeem
On Sat, Feb 18, 2012 at 7:27 PM, Justin A. Lemkul wrote:
>
>
> shahid nayeem wrote:
>
>> Dear All
>>
>> I am doing umbrella sampling for a protein complex. After analysis I am
>> finding that prifle.xvg has not converged. Now I want to
sampling.
Please suggest.
How one should ascertain the initial box size so that g_wham gives a
converged profile.xvg.
Please help.
Shahid nayeem
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Dear All
How does the terminal group capping/ionization state will influence the
Free energy obtained from g_wham in umbrella sampling simulation.
Shahid Nayeem
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histo.xvg and profile.xvg , it cost a lot computationally and if you
don't get it right these computational resources are wasted.
Shahid nayeem
On Mon, Feb 13, 2012 at 8:12 PM, Justin A. Lemkul wrote:
>
>
> shahid nayeem wrote:
>
>> Thanks for quick reply. I have created
Create a file named input.g_rms. write the group number in this file. In
your shell script after command line write wrote:
> Hi,
>
> I'm not good at shell programming now.
> For the simplicity, I wrote down all the gromacs commands in one shell
> script.
>
> It means that if I execute the .sh fil
my
case. Thanks for any help.
Shahid Nayeem
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.
shahid Nayeem
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lease
respond. Please suggest where else I should search for these.
Thanking all
shahid Nayeem
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P
I can compare side chain configuration of trajectory with
bound and unbound sidechain configuration. Please help.
Shahid Nayeem
On Tue, Nov 15, 2011 at 7:02 PM, felmer...@uchile.cl wrote:
> In any case, if you really want to see flexibility then you need RMSF and
> not RMSD as the later wil
Dear all
I am interested to get contour plot of residue RMSD vs time graph. I want
to get the flexible and rigid regions of protein chain during simulation.
g_rmsf does not gives me this plot.
Please help
shahid Nayeem
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on
this list to tell that how should I attempt this problem.
Shahid Nayeem
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Please don't pos
is a big
protein so long MD simulation is not possible. Short duration MD will be
insufficient to search native structure. I am stuck-up. Can anyone on this
list help me.
Shahid Nayeem
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Please
I tried with single Arginine molecule pdb.
pdb2gmx -f arg.pdb -o arg.gro -p arg.top
genconf -f arg.gro -nbox 2 2 2 -o seq.gro
genbox -cp seq.gro -cs spc216.gro -ci protein.pdb -nmol 1 -o seq_box.gro
-box 1.8 1.8 1.8
command runs but it does not add protein.pdb to the box
shahid nayeem
On Fri, Aug
along with
protein.
shahid nayeem
On Thu, Aug 11, 2011 at 3:15 PM, Mark Abraham wrote:
> On 11/08/2011 7:24 PM, shahid nayeem wrote:
>
> Hi Justin
> I prepared a box of SOL and arginine Hydrochloride. But when I solvate my
> protein with this box now the positively charged argini
Both files hist.xvg and profile.xvg both are simultaneous output of this
command. I did not run it twice, once to get profile.xvg and then to get
hist.xvg as you uderstood.
On Thu, Aug 11, 2011 at 5:42 PM, Justin A. Lemkul wrote:
>
>
> shahid nayeem wrote:
>
>> I used
I used following command
g_wham_4.5.4 -it tpr-files.dat -if pullf-files.dat -o hist -unit kCal
Both profile.xvg and hist.xvg are created with this command using same
pullf.xvg and .tpr files.
shahid Nayeem
On Thu, Aug 11, 2011 at 5:07 PM, Justin A. Lemkul wrote:
>
>
> shahid nay
a box was without
error. which forcefield in gromacs has inbuilt .itp file for free amino acid
which I can include in my .top file.
Shahid Nayeem
On Fri, Jul 29, 2011 at 5:02 PM, Justin A. Lemkul wrote:
>
>
> shahid nayeem wrote:
>
>> Dear All I am trying to find the topology a
be needed.
shahid Nayeem
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Dear All
I am trying to find the topology and parameterof free Arginine Hydrchloride
molecule in gromacs force-field format. Developing it in Pro-Drg will not
serve as I will need some other parametrization tool to check it charges.
If someone can help, I will be grateful.
shahid Nayeem
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Dear Justin
Here is my histogram file which does not show any window overlap. The
sampling window I choose was 0.2 nm which I think is very large. Please
suggest.
Shahid nayeem
hist.xvg
Description: Binary data
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two dips in PE
curve. Please see it and tell me why I am getting these dips.
Shahid Nayeem
profile.xvg
Description: Binary data
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this in gromacs then
what should be the .mdp file for such increment in temperature at regular
intervals.
Thanks for any help.
Shahid Nayeem
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does gives an oitput of summary_distance.dat. It has
one column of conf.gro number but no distance. Where I am wrong.
Shahid Nayeem
On Tue, Apr 19, 2011 at 6:20 PM, Justin A. Lemkul wrote:
>
>
> Justin A. Lemkul wrote:
>>
>>
>> shahid nayeem wrote:
>>>
>>
Hi Justin
Thanks a lot. What is the purpose of adding 100mM NaCl. Is it
mimicking physiological condition.
Shahid Nayeem
On Tue, Apr 19, 2011 at 5:47 PM, Justin A. Lemkul wrote:
>
>
> shahid nayeem wrote:
>>
>> Hi Justin
>> I went through your tutorial of umbrella sa
groups are created. Does index.ndx should contain all
residue from the chain which has to move or few are sufficient.
Shahid Nayeem
On Thu, Apr 14, 2011 at 6:34 PM, Justin A. Lemkul wrote:
>
>
> shahid nayeem wrote:
>>
>> Dear All
>> I have some protein complex pdb afte
Dear All
I have some protein complex pdb after docking two monomers. The
scoring of these docked structure are not true representative of
binding affinity. I want calculate the binding affinity affinity of
these docked pdb. Can anyone suggest me, how should I proceed.
Shahid Nayeem
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gromacs trajectory analysis where I can do
backbone fitting first and then translate to coincide CA of residue of
interest before calculating RMSD.
Shahid Nayeem
On Thu, Feb 24, 2011 at 7:14 PM, Justin A. Lemkul wrote:
>
>
> shahid nayeem wrote:
>>
>> Dear All
>>
>>
clarification is that in gromacs g_cluster how can I use
greedy algorithm for clustering.
Shahid Nayeem
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in full.mdp
Please suggest what should I do .
For a single chain I did MD keeping backbone fixed and allowing side
chain free movement. In my posres.itp I used a force of 2000 kj to
keep them in fixed position with option genrestr -fc.
Waiting for reply
Shahid Nayeem
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Dear All
If any one is aware of a server on which one can upload job for
running Gaussian, Please let me know. This I need to modify charges in
the topology file created by ProDrg server.
Shahid Nayeem
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rsh treatment of system then suggest me
the way out.
My sa.mdp sa_hot.mdp and sa_equilibriation.mdp as well as chaps.itp
are attached with this mail
Shahid Nayeem
On Mon, Jan 31, 2011 at 9:47 AM, Justin A. Lemkul wrote:
>
>
> shahid nayeem wrote:
>>
>> Please tell me where I am wr
That means in energy group in .mdp file I should write interface.ndx
and tell me if on interface there is hydrogen bond then its value I
will get or not.
Shahid Nayeem
On Mon, Feb 7, 2011 at 6:50 PM, Justin A. Lemkul wrote:
>
>
> shahid nayeem wrote:
>>
>> Dear User
>&g
.
Thanking you
Shahid Nayeem
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potential energy. Then as suggested by Justin I used
smaller box and there also in simulated annealing stage the system
gives linc warning and the programme stops with fatal error. Please
tell me where I am wrong.
shahid nayeem
On Fri, Jan 28, 2011 at 10:59 AM, Mark Abraham wrote:
> On 28/01/2011 3
warning in 0 step with rms 7407.805164, max 66989.116545 (between atom
94 and 117) and a list of bond thar rotated more than 30 degree almost
atom number belonging to chaps molecule.
Please help.
shahid Nayeem
On Thu, Jan 27, 2011 at 7:06 PM, Justin A. Lemkul wrote:
>
>
> shahid nayeem wrote:
&
pressure 100 bar, then 1ns
simulated annealing from temp. 0k to 300k and then ins equilibriation
at this temperature. In case of urea finally I got uniformly solvated
urea_water_box but in chaps I couldn’t get it.
Shahid Nayeem
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http
I forgot to mention that when I prepared urea_water box then also I got
similar box of water in one region and urea in other region separated from
it. But on minimization and following simulated annealing
and equilibration I got a uniformly mixed urea water box.
Shahid Nayeem
On Thu, Jan 27, 2011
but not
inside water. I should have visualized it earlier before going for
minimization. Please help me.
shahid Nayeem
On Thu, Jan 27, 2011 at 11:36 AM, Mark Abraham wrote:
>
>
> On 01/27/11, *shahid nayeem * wrote:
>
> Dear All
> I am trying to prepare a solvation box of chaps
should I do.
Shahid nayeem
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Dear Gmx User
I want to prepare a solvation box for say 50mM chaps solution. The density
is not known. How should I start calculating the number of chaps molecule
and number of water molecule required for say 6X6X6 size box, which after
equilibriation should give the exact strength of the solution.
interaction between the two
molecule. Please suggest me, how can I do this.
Thanking you.
Shahid Nayeem
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Dear Gromacs User
My pdb is homodimer with Arg as c-terminal residue. With this pdb I am
etting following error in pdb2gmx command
Program pdb2gmx, VERSION 4.0.7
Source code file: pdb2gmx.c, line: 429
Fatal error:
Atom OXT in residue ARG 107 not found in rtp entry with 17 atoms
while
while
running grompp. Please suggest me what should I do.
Shahid Nayeem
On Thu, Nov 25, 2010 at 3:12 AM, Erik Marklund wrote:
> shahid nayeem skrev 2010-11-24 18.02:
>
> Dear all
>> I am trying MD of cyt C containing heme. I am able to generate bonds with
>> specbond.dat by
I am using ffG43a1 forcefield. its .rtp file contains topology of Heme but
Met SD and FE bond is not there.
Shahid Nayeem
On Thu, Nov 25, 2010 at 5:11 AM, Justin A. Lemkul wrote:
>
>
> Erik Marklund wrote:
>
>> shahid nayeem skrev 2010-11-24 18.02:
>>
>>> Dea
parameter
for these bonds but I couldnt get it. If someone on this mailing list can
help me I will be grateful. Cyt C is very widely modelled protein with
Gomacs in literature hence I expect to get some help from the forum.
shahid nayeem
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Dear All
How can I follow the changes in native contacts of protein unfolding
trajectory. Is it g_mdmat, if so then how to analyze the results obtained
from this command.
Shahid Nayeem
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Please
ried to
find these bonds in in built files of gromacs i.e. /share/top/ but I
couldnt. Can any one help me and tell me where can I find these bonds/angle
parameters and what should I add in ffG43a1 .itp .rtp files
please help.
Shahid Nayeem
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ht
ried to
find these bonds in in built files of gromacs i.e. /share/top/ but I
couldnt. Can any one help me and tell me where can I find these bonds/angle
parameters and what should I add in ffG43a1 .itp .rtp files
please help.
Shahid Nayeem
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ht
ried to
find these bonds in in built files of gromacs i.e. /share/top/ but I
couldnt. Can any one help me and tell me where can I find these bonds/angle
parameters and what should I add in ffG43a1 .itp .rtp files
please help.
Shahid Nayeem
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ht
ugh .top file shows these bonds the .gro file generated does not
show these bonds in VMD while original pdb file shows these bonds.
thanking you.
waiting for your suggestion.
shahid Nayeem
On 7/15/10, Justin A. Lemkul wrote:
>
>
> shahid nayeem wrote:
>> Hi Justin
>> These err
your suggestion to proceed further.
shahid Nayeem
On 7/15/10, Justin A. Lemkul wrote:
>
>
> shahid nayeem wrote:
>> Dear All
>> I used the following command sequentially to prepare file for energy
>> minimization and subsequent MD run.
>> 1. pdb2gmx -f *.pdb -o
were 9 errors in input file(s)
---
pdb2gmx works properly using ff43a1 forcefield. My protein contains
Heme. I was having N-terminal ACE group which I simply deleted from
the pdb.
Am I right in deleting this group. How should I proceed to get rid of
this error.
Thanks in anticipation of help.
Shahid Nay
6223 3
0.0510077 0.0234374 4 0.0512037 0.0234554 5 0.0284763 0.0401088 6
0.236609 0.108979
Tghe first column is atom no. and what are the values in two columns. I want
average solvent accessible surface area of each atom of my protein in whole
trajectory.
Shahid Nayeem
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Hi
No i dont have any capping group
shahid Nayeem
On 5/24/10, Justin A. Lemkul wrote:
>
>
>
> shahid nayeem wrote:
>
>> Hi Justin
>> I choose group 5 main chain for dssp calculation
>>
>
> Do you have any capping groups (N-acetyl, C-amine, etc)?
>
>
Hi Justin
I choose group 5 main chain for dssp calculation
Shahid Nayeem
On 5/24/10, Justin A. Lemkul wrote:
>
>
>
> shahid nayeem wrote:
>
>> Dear All
>> I did 10ns simulation of three peptide residue solvated in water. Each
>> peptide residue is 26 resid
edure for full protein molecule simulation I get
the same number of residue in dssp output as well as final.gro file
shahid nayeem
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time0.000
Warning: if there are broken molecules in the trajectory file,
they can not be made whole without a run input file
Back Off! I just backed up dd8G1JXX to ./#dd8G1JXX.1#
Segmentation fault
shahid
On 5/18/10, Justin A. Lemkul wrote:
>
>
>
> shahid nayeem wr
backing up the previous one. Then I moved
all the files of dssp directory to /usr/local/bin/ and then tried to run
do_dssp I am in the same situation.
waiting for your help
shahid nayeem
On 5/18/10, Justin A. Lemkul wrote:
>
>
>
> shahid nayeem wrote:
>
>> Dea
/local/bin/ and I couldnt find. I
even tried dsspcmbi.zip file but again I got the same error. I
compiled dssp as root. Now what shoul I do in order to run do_dssp
comand of gromacs.
Shahid nayeem
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Dear all
I downloaded xmgr-4.1.2.tar.gz and tried to install by following commands.
tar -xvzf xmgr-4.1.2.tar.gz
cd xmgr-4.1.2
./configure
make
make install
But it gives error command xmgr not found.
Please help.
shahid Nayeem
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http
.
shahid Nayeem
On 5/12/10, Ran Friedman wrote:
>
> Hi,
>
> There's no recipie to locate aggregation hot spots based on MD
> simulations. There are many papers on simulations of protein and peptide
> aggregation from which you can draw some ideas, but bear in mind that
> agg
Dear all
What are the analysis tools which should be used on MD trajectory file in
order to find potential aggregation sites of a protein. Anyone can tell me
about specific resource material on use of Gromacs to predict protein
aggregation hot spots from MD trajectory anlysis.
Shahid Nayeem
-cpi flag. I require answer
of my question regardless of the use of .cpt file.
shahid nayeem
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Please search the archive at http://www.gromacs.org/search before posting!
Please don't pos
Hi Mark
How one should be certain that this much trajectory is long enough to get
coverged ensemble.
Shahid
On 4/27/10, Mark Abraham wrote:
>
> On 27/04/2010 8:58 PM, Justin A. Lemkul wrote:
>
>>
>>
>> shahid nayeem wrote:
>>
>>> Dear Mark
>&
Hi Justin
Should I try to do position restraint at 500k and then full MD simulation.
shahid
On 4/27/10, Justin A. Lemkul wrote:
>
>
>
> shahid nayeem wrote:
>
>> My peptide is 26 residue alpha helix obtained from crystal structure .pdb
>> file. I am posting en
; Isotropic pressure coupling is now on
Pcoupl = berendsen
Pcoupltype = isotropic
tau_p = 0.5
compressibility = 4.5e-5
ref_p = 1.0
; Generate velocites is off at 500 K.
gen_vel = no
gen_temp = 500.0
gen_seed = 173529
shahid
On 4/27/10, Justin A. Lemkul wrote:
>
>
>
> shahid
/10 13:16, shahid nayeem wrote:
>
>> Dear All
>> I am trying to study inter peptide interaction fpr which I need to put
>> more than one peptide in one simulation box. I did it with genconf
>> command but this inserts peptide in a regular ordered manner I want
>&
than one residue in insert molecule.
Please help me and write commands which I should follow.
Shahid Nayeem
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Please don
I was also trying to put more than one protein in one simulation box. I was
able to do it with genconf but it appears that the addition is in very
ordered manner if one looks .gro file in VMD. How can I add these protein in
disordered random orientation.
msnayeem
On 4/20/10, Justin A. Lemkul wro
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