Re: [ccp4bb] MD program suitable to compute trajectories of a very small molecule in a protein

[Amit Singh]

Dear Fred,

Please follow the instructions below to install Gromacs on your CentOS
system without any other prerequisite.

https://centos.pkgs.org/7/epel-x86_64/gromacs-2018.8-1.el7.x86_64.rpm.html


On Thu, 23 Jan, 2020, 4:51 pm Tanner, John J., 
wrote:

> Fred,
>
> You might want to review the literature on using MD to study diffusion of
> O2/CO in myoglobin.
>
> Jack
>
> John J. Tanner
> Professor of Biochemistry and Chemistry
> Associate Chair of Biochemistry
> Department of Biochemistry
> University of Missouri
> 117 Schweitzer Hall
> 503 S College Avenue
> Columbia, MO 65211
> Phone: 573-884-1280
> Email: tanne...@missouri.edu
> http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html
> Lab: Schlundt Annex rooms 3,6,9, 203B, 203C
> Office: Schlundt Annex 203A
>
> On Jan 23, 2020, at 3:43 AM, Fred Vellieux 
> wrote:
>
> Dear all,
>
> I need to run MD calculations in order to follow the trajectories of a
> very small molecule inside a protein. From previous calculations (not MD) I
> have starting positions for this small molecule that all seem in agreement
> with a possible path of motion inside the protein.
>
> Now I need to access a MD program (without licensing costs).
>
> I've had a look at the software list provided in Wikipedia (and tried to
> install the software, in succession, alas without success):
>
> cp2k - present for CentOS6 (with yum install ?) but appears to have
> vanished for CentOS7;
>
> gromacs requires a gcc version I don't have (even after having compiled
> and installed a suitable gcc version, cmake complains about the "old
> version" and stops);
>
> NWChem is unhappy with the Python setup and doesn't compile.
>
> I don't know how to solve all these OS version, library, unsuitable binary
> etc problems. In fact I don't know if any of these 3 software suites would
> be suitable for what I have in mind.
>
> Hence would anyone know of a useful MD software suite that would be
> suitable for my purpose and comes with statically linked binaries suitable
> for Intel 64 (Linux) ? Just launch the executable and it runs, no questions
> asked...
>
> Thank you,
>
> Fred.
>
> 
>
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>
>
>
> --
>
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Re: [ccp4bb] MD program suitable to compute trajectories of a very small molecule in a protein

[Tanner, John J.]

Fred,

You might want to review the literature on using MD to study diffusion of O2/CO 
in myoglobin.

Jack

John J. Tanner
Professor of Biochemistry and Chemistry
Associate Chair of Biochemistry
Department of Biochemistry
University of Missouri
117 Schweitzer Hall
503 S College Avenue
Columbia, MO 65211
Phone: 573-884-1280
Email: tanne...@missouri.edu
http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html
Lab: Schlundt Annex rooms 3,6,9, 203B, 203C
Office: Schlundt Annex 203A

On Jan 23, 2020, at 3:43 AM, Fred Vellieux 
mailto:frederic.velli...@lf1.cuni.cz>> wrote:

Dear all,

I need to run MD calculations in order to follow the trajectories of a very 
small molecule inside a protein. From previous calculations (not MD) I have 
starting positions for this small molecule that all seem in agreement with a 
possible path of motion inside the protein.

Now I need to access a MD program (without licensing costs).

I've had a look at the software list provided in Wikipedia (and tried to 
install the software, in succession, alas without success):

cp2k - present for CentOS6 (with yum install ?) but appears to have vanished 
for CentOS7;

gromacs requires a gcc version I don't have (even after having compiled and 
installed a suitable gcc version, cmake complains about the "old version" and 
stops);

NWChem is unhappy with the Python setup and doesn't compile.

I don't know how to solve all these OS version, library, unsuitable binary etc 
problems. In fact I don't know if any of these 3 software suites would be 
suitable for what I have in mind.

Hence would anyone know of a useful MD software suite that would be suitable 
for my purpose and comes with statically linked binaries suitable for Intel 64 
(Linux) ? Just launch the executable and it runs, no questions asked...

Thank you,

Fred.



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Re: [ccp4bb] MD program suitable to compute trajectories of a very small molecule in a protein

[Abhik Mukhopadhyay]

Dear Fred,
Have you tried NAMD

https://www.ks.uiuc.edu/Research/namd/

Abhik


On Thu, Jan 23, 2020 at 9:43 AM Fred Vellieux 
wrote:

> Dear all,
>
> I need to run MD calculations in order to follow the trajectories of a
> very small molecule inside a protein. From previous calculations (not
> MD) I have starting positions for this small molecule that all seem in
> agreement with a possible path of motion inside the protein.
>
> Now I need to access a MD program (without licensing costs).
>
> I've had a look at the software list provided in Wikipedia (and tried to
> install the software, in succession, alas without success):
>
> cp2k - present for CentOS6 (with yum install ?) but appears to have
> vanished for CentOS7;
>
> gromacs requires a gcc version I don't have (even after having compiled
> and installed a suitable gcc version, cmake complains about the "old
> version" and stops);
>
> NWChem is unhappy with the Python setup and doesn't compile.
>
> I don't know how to solve all these OS version, library, unsuitable
> binary etc problems. In fact I don't know if any of these 3 software
> suites would be suitable for what I have in mind.
>
> Hence would anyone know of a useful MD software suite that would be
> suitable for my purpose and comes with statically linked binaries
> suitable for Intel 64 (Linux) ? Just launch the executable and it runs,
> no questions asked...
>
> Thank you,
>
> Fred.
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>



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[ccp4bb] MD program suitable to compute trajectories of a very small molecule in a protein

[Fred Vellieux]

Dear all,

I need to run MD calculations in order to follow the trajectories of a 
very small molecule inside a protein. From previous calculations (not 
MD) I have starting positions for this small molecule that all seem in 
agreement with a possible path of motion inside the protein.


Now I need to access a MD program (without licensing costs).

I've had a look at the software list provided in Wikipedia (and tried to 
install the software, in succession, alas without success):


cp2k - present for CentOS6 (with yum install ?) but appears to have 
vanished for CentOS7;


gromacs requires a gcc version I don't have (even after having compiled 
and installed a suitable gcc version, cmake complains about the "old 
version" and stops);


NWChem is unhappy with the Python setup and doesn't compile.

I don't know how to solve all these OS version, library, unsuitable 
binary etc problems. In fact I don't know if any of these 3 software 
suites would be suitable for what I have in mind.


Hence would anyone know of a useful MD software suite that would be 
suitable for my purpose and comes with statically linked binaries 
suitable for Intel 64 (Linux) ? Just launch the executable and it runs, 
no questions asked...


Thank you,

Fred.



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