[gmx-users] gmx_clusterByFeatures - Features Based Conformational Clustering of MD trajectories

[rajendra kumar]

Dear GROMACS users,

I have developed a tool (hybrid C++ and Python) for features-based
conformational clustering of MD trajectories. Its source code is available
here: https://github.com/rjdkmr/gmx_clusterByFeatures. For
more detail about the tool, please visit here:
https://gmx-clusterbyfeatures.readthedocs.io. It is very easy to install
(sudo pip3 install gmx-clusterByFeatrues).

I have also presented an example to cluster ligand conformations with
respect to receptor (
https://gmx-clusterbyfeatures.readthedocs.io/en/latest/examples/ligand_cluster.html
).I am also working on other examples.

Feedback are welcome.

Thanks and regards,
Rajendra

--

|==|
|* Dr. Rajendra Kumar   *|
| Post-Doctoral Researcher |
| Department of Chemistry  |
| Umeå University <http://www.umu.se/english/>, |
| Umeå, Sweden.|
|==|
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Re: [gmx-users] Groove width

[rajendra kumar]

On Mon, Jun 4, 2018 at 1:10 PM,  wrote:

> Hii
>> I have tried installation of do_x3dna in ubuntu system following the
>> instructions given in the link. Installation done successfully then I
>> have written the path of do_x3dna in .bashrc file(export
>> do_x3dna=/usr/local/do_x3dna/bin/) and source the file source ~/.bashrc.
>> Then I tried doing do_x3dna -h but it shows do_x3dna not found. What is
>> wrong here? My GROMACS version is 2016.3 . Need suggestion .
>>
>
​You do not have to give -DCMAKE_INSTALL_PREFIX option. Without this
option, do_x3dna will be installed in default directory and It will run
without any additional step.
For questions relating to do_x3dna, please use do_x3dna forum (
https://groups.google.com/forum/#!forum/do_x3dna).
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Re: [gmx-users] Groove width

[rajendra kumar]

>
>
> I am doing simulation of DNA molecule. I want to calculate groove width of
> DNA in GROMACS. How to do this? Someone please help.
>
>
​You may use do_x3dna (http://do-x3dna.readthedocs.io). It uses 3DNA in
background and works with GROMACS files.​ Package also includes tools to
analyze the large data generated from MD trajectories.
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Re: [gmx-users] Use pdb file generated with Maestro, in Gromacs

[rajendra kumar]

Hi,

As suggested above, use -ignh to ignore hydrogen atoms. To use a specific
Histidine, you may change residue name HIS to HIP(Amber)/HSP(Charmm)/HISH(
​OPLS​
) or HID(Amber)/HSD(Charmm)/HISD(
​OPLS​
) or HIE(Amber)/HSE(Charmm)/HISE(
​OPLS​
) either in PDB file or interactively through pdb2gmx usng -his command.


On Wed, Mar 30, 2016 at 12:27 PM, bio hpc  wrote:

> Hi,
>
> we have created some protein pdb files with Maestro. When we try to un an
> MD simulation with gromacs, we get errors like:
>
> >> Atom HD11 in residue ASN 5 was not found in rtp entry ASN with 14 atoms
>
> I tried to find a solution and it seems that internal gromacs dictionary
> for hydrogens is different from the one from Maestro and other formats. It
> seems, from what I read, that one must convert all hydrogen types to
> Gromacs format. Is is there any script that can do this automatically?
>
> Of course, there is the option “ignore hydrogens”, but this would be bad
> for us, since we need some histidines in the binding site, and so on.
>
> Thanks,
> BIO-HPC
>
>
>
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Re: [gmx-users] Query on g_mmpbsa in gromacs

[rajendra kumar]

Pairwise interaction scheme
 ​
is not implemented in g_mmpbsa. Therefore, g_mmpbsa cannot be used to
calculate interaction energy between two residues.

With best regards,
​Rajendra

​

On Mon, Mar 28, 2016 at 2:37 PM, Prasanna Dr 
wrote:

> Hi
>
> I have been using g_mmpbsa of Rashhmi Kumari and group to calculate binding
> energy of lipids in protein-lipid complex. I got a quite good results with
> g_mmpbsa. Now, In my next step I need to perform network analysis where
> pairwise interaction energy from mmpbsa will be considered.
>
> I have 450 aminoacids and 2 lipids in the system. After mmpbsa i have
> generated residue decomposition energy of aminoacids with lipid (not
> between aminoacids) as shown below  (for example purpose)
>
> 11.0784
> 2-0.0261
> 30.9493
> 40.0206
> 5-0.0583
> 60.0061
> 7-0.0278
> .
> .
> .
> 450
>
> While running mmpbsa my first input was protein and second input was lipid
> (in place of ligand). Now I have interaction energy of each aminoacid with
> lipid .
>
> Now,  I need interaction energy between aminoacids. like 1st aminoacid with
> remaining 499  aminoacid and 2nd with remaining 499 aminoacids and so on.
>
> Is it possible to calculate interaction energy between amnoacids and with
> lipids using g_mmpbsa (n X n matrix of energy values) ?
>
> --
> D R Prasanna
> Research Scholar
> Computational  Biophysics Group
> Department of Biotechnology
> Indian Institute of Technology Madras
> Chennai
> Tamilnadu-600036
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Re: [gmx-users] g_mmpbsa positive binding energy

[rajendra kumar]

Hi,

MM/PBSA method has several limitations (discussed in several publications)
and therefore, you may be getting positive energy values from these
limitations. You may get a negative binding energy after further increasing
the dielectric constant, however, interpretation of this value would be
very difficult. g_mmpbsa calculates
​​
binding Enthalpy. It can be used to compare binding of several small
ligands with same receptor protein because one may assume that entropy
change is almost similar or negligible in all complexes. In case of
​ ​
large molecules binding,
​ ​
​

​binding
comparison
​s​
​are highly unreliable ​as entropy cannot be neglected
.
​ Because of these reasons, I would not use MM/PBSA method for
protein-protein complex.​


Regards,
Rajendra
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Re: [gmx-users] g_mmpbsa time

[rajendra kumar]

You may use -dt as option in g_mmpbsa. For example, -dt 600 or -dt 120 .


On Thursday, September 17, 2015 at 7:41:25 AM UTC+2, elham wrote:
>
> Dear users
> i simulated a system for 30 nano-seconds(dt=2fs) and my frame was 6 ps
> for binding free energy computations by g_mmpbsa method in gromacs, my 
> computations took a long time
> is it correct?
> can i change my simulation time in *mdp* file for *tpr* production for  
> using in g_mmpbsa calculations or it s equal to  the time of my 
> siulation ???
> regards
>
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Re: [gmx-users] Force field For Protein-Ligand Complex

[rajendra kumar]

You may also use Amber99sb-ildn and GAFF for protein and ligand,
respectively. You can find method in this paper:
http://pubs.acs.org/doi/full/10.1021/ci500020m. Although, AM1-BCC method
was used for charge calculations, I would suggest to use RESP method.


With best regards,
Rajendra
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[gmx-users] g_distMat: A tool to calculate average min-distance matrix on multiple CPU cores

[rajendra kumar]

Dear GROMACS Users,

I have wrote a small tool g_distMat (https://github.com/rjdkmr/g_distMat).
It is almost similar to the g_mdmat.

Features:
 Average minimum-distance matrix (residue-wise) between two index groups
 Related Standard deviation and variance matrix
 Fraction of Contacts(map) over the trajectory for residues that are
within cut-off distance
 Parallel Calculation: uses multiple cores of CPU. Multi-threading using
pthread library.


With best regards,
Rajendra
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