Hey all,
I'm trying to simulate a peptide-protein docked complex. I docked the
peptide using pepATTRACT package. After analysis, I selected the best
pose and tried to simulate. This yielded an error and got core dumped
in NVT equilibriation.
I'm using GROMOS 54a7 force field. The error is pasted
y Mark,
Thanks for the suggestion. I'll try recompiling the package.
Best,
Azeem
>
> Mark
>
> On Wed, Apr 18, 2018, 05:37 Syed Azeem wrote:
>
>> >> Hey Mark,
>> >>
>> >> Still the same problem persists.
>> >>
>> >>
>&
>> Hey Mark,
>>
>> Still the same problem persists.
>>
>>
>>
> Hi,
>
> That looks like a broken build of GROMACS, rather than a bug in the code or
> a broken file. Can you try those gmx check commands on another installation
> somewhere else? (Also gmx check -m doesn't do anything useful any more,
o find out e.g. whether they are trajectories that
> have matching numbers of particles, etc.
>
> Mark
>
> On Tue, Apr 17, 2018 at 1:13 PM Syed Azeem
> wrote:
>
>> > Hi,
>> >
>> > What does gmx check report on the two input .xtc files?
>>
>> Hey
]
7ffc7233b000-7ffc7233e000 r--p 00:00 0 [vvar]
7ffc7233e000-7ffc7234 r-xp 00:00 0 [vdso]
ff60-ff601000 r-xp 00:00 0
[vsyscall]
Aborted (core dumped)
>
> Mark
>
> On Tue, Apr 17, 2
Hey all,
I'm experiencing an error while using trjcat command. Initially, I ran
a simulation for 50 ns and then extended till 100ns. After extension,
I concatenated the trajectories of both the runs using gmx trjcat.
Then, again I extended the run from 100 ns to 500 ns. Finally, I tried
to concat
Hi all,
I tried installing Gromacs 2016.4 on a new hardware with Nvidia Quadro
K420 2gb support.
Installation completed successfully following Quick and Dirty method.
But gmx is not working.
Error says:
gmx: error while loading shared libraries: libnvidia-ml.so.1: cannot
open shared object file
> Hi All,
>
> I have run an extended simulation for 90ns like this: (my previous run was
> for 10ns)
>
> grompp -f new.mdp -c old.tpr -o new.tpr
> mdrun -s new.tpr -cpi old.cpt
>
> I output mdrun STDOUT to an output file and it looks like this:
>
> ##
>
>
> Dear all,
> I have done md simulation at 1 bar pressure but after the simulation when i
> plot the pressure graph, plot shows fluctuation range from -200 to 200 bar.
> Is this fluctuation is acceptable?
Hey,
This is quite normal. see:
http://www.gromacs.org/Documentation/Terminology/Pressure
>
> Hi,
>
> On Wed, Jun 21, 2017 at 12:47 PM Syed Azeem
> wrote:
>
>> Hi all,
>>
>> I installed gromacs 5.1.2 on a new machine.
>> Config: Intel Core i5 6500 3.20 GHz Quad Core Skylake with 8 GB DDR4.
>>
>> Then I started a NVT simulation fo
Hi all,
I installed gromacs 5.1.2 on a new machine.
Config: Intel Core i5 6500 3.20 GHz Quad Core Skylake with 8 GB DDR4.
Then I started a NVT simulation for 500ps with ~25 atom system.
Surprisingly, the estimated time was 4 days and 3 hours.
There was a note stating consider rebuilding gmx
> On 5/31/17 8:26 AM, Syed Azeem wrote:
>>> On 5/29/17 8:00 AM, Syed Azeem wrote:
>>>> Hey all,
>>>>
>>>> I simulated a protein-peptide docked complex. Post simulation, I
>>>> created an index file selecting only the Protein Group
>
> On 5/29/17 8:00 AM, Syed Azeem wrote:
>> Hey all,
>>
>> I simulated a protein-peptide docked complex. Post simulation, I
>> created an index file selecting only the Protein Group
>> (protein-peptide complex). Then using editconf, I created a .pdb file
>&
Hey all,
I simulated a protein-peptide docked complex. Post simulation, I
created an index file selecting only the Protein Group
(protein-peptide complex). Then using editconf, I created a .pdb file
for the same.
When I view the prtn.pdb file, only the protein is available but not
the peptide. St
y have to either be in the force field already, or added to it.
> If they are not present in amber99sb-ildn, then you need to understand how
> the topologies were generated and how they are intended to be used in order
> to make an appropriate choice.
>
> Mark
>
> On Fri,
Hi all,
I'm trying to simulate a Protein-Peptide docked complex.
I used Amber99sb-ildn ff with TIP3P. Since mine is a docked complex,
two separate topology and position restraint files were created as
chains A & B, automatically.
When I tried to generate the .tpr file for adding ions to the syste
2gmx just rebuilt them so
> you
> didn't have to waste time renaming all your non-conforming H atoms.
>
> -Justin
Now I understood the -ignh option.
Thanks for the explanation
-Azeem
>>>> On Mar 1, 2017, at 10:22, Syed Azeem
>>>> wrote:
>>>>
>
> Use -ignh in pdb2gmx.
Hi Reza,
I tried -ignh, it's working fine.
But i need to calculate H-bonds after docking the same peptide. Then
the same error will crop up and I won't be able to calculate H-bonds.
>> On Mar 1, 2017, at 10:22, Syed Azeem wrote:
>>
>&g
Hi all,
I tried passing a predicted peptide (16-mer) into GMX and ended up
with a fatal error regarding hydrogen. I tried ignoring the hydrogens
using -ignh command. But I'll need to calculate H-bonds for the next
analysis, as I'll dock this peptide into a target protein.
Fatal error:
Atom HB3 in
;>
>>> In GROMACS implicit solvent is depreciated, so you should either use
>>> explicit solvent, or pick a different MD engine if you want implicit.
>>> 23.12.2016 18:00, gromacs.org_gmx-users-requ...@maillist.sys.kth.se
>>> ?:
>>> Message: 1
the model.
>
>In GROMACS implicit solvent is depreciated, so you should either use
>explicit solvent, or pick a different MD engine if you want implicit.
>23.12.2016 18:00, gromacs.org_gmx-users-requ...@maillist.sys.kth.se ?:
> Message: 1
> Date: Fri, 23 Dec 2016 16:25:33 +0530
Hi all,
What's the difference between Implicit and Explicit solvation?
Is there any difference in setting up the system for simulation?
Which is computationally effiecient?
Thanks in advance
Azeem
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ral Research Associate
> University of Tennessee/Oak Ridge National Laboratory
> Center for Molecular Biophysics
>
>
>> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
>> on behalf of Syed Azeem
>>
>> Sent: Thursday, Dec
Hi all,
What are criteria for choosing the force fields?
Is choosing a force field for a particular protein molecule, a trial
and error method based?
Thanks in advance
Azeem
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to be. It is a reasonable trial and error guess aimed at
>> computational efficiency, e.g. not exceeding a certain amount of
>> computational burden for really bad structures. Alternatively, limiting
>> the number of minimization steps can help not produce some kind of a
>> fr
.gromacs.org/Support/Mailing_Lists
>>>>>
>>>>> * For (un)subscribe requests visit
>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>>>> send a mail to gmx-users-requ...@gromacs.org.
>>>>>
>>&g
Hi all,
What is the basis of inputting the maximum number of energy
minimization steps in GROMACS?
Does maximum number of energy minimization steps depend on the number
of residues?
I came across many articles wherein the authors have described the
number of energy minimization steps within which
Hello All,
I'm trying to simulate a Protein-Peptide complex using GROMACS 5.1.4.
For reference, I referred Justin Lemkul's Tutorial for Protein Ligand
complexes. In which, the topology for ligand (small molecule) was
generated using PRODRG.
In my case, do I need to treat my peptide (16-mer) in su
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