[gmx-users] PCA and FEL

[sun]

Hello everyone
I am using Gromacs 5.0 for protein-ligand MD. I want to do FEL analysis for the stability of my pro-lig complex. In a 2015 paper, The group calculated two principal component, PC1 and PC2 and then prepared an.xvg file to be used as input for g_sham. My question is, when we use g_anaeig; we get eigenvec.xvg. from -comp flag. Now how shall one select two principal components from that data? I am sorry if my question is wrong but please help me.

My second question is, can we use any two parameters like rmsd and Rg for input in g_sham to probe the stability of complex? Is that valid?

With Regards
Suniba

Sent from my iPhone

[Tsjerk Wassenaar]

Hi Suniba,

No, with gmx anaeig you can select -2d, which does a 2D projection onto the
selected eigenvectors. Alternatively, you can combine any two projections
onto eigenvectors, which you get using the option -proj. The quickest way
to do that is something like:

paste <(grep -v '^[@#]' proj1.xvg) <(proj2.xvg) | awk '{print $2, $4}' >
combined.xvg

You will loose the labels, but that should be fine.

You can combine other variables in a similar manner.

Hope it helps,

Tsjerk

Post by sun
Hello everyone
I am using Gromacs 5.0 for protein-ligand MD. I want to do FEL analysis
for the stability of my pro-lig complex. In a 2015 paper, The group
calculated two principal component, PC1 and PC2 and then prepared an.xvg
file to be used as input for g_sham. My question is, when we use g_anaeig;
we get eigenvec.xvg. from -comp flag. Now how shall one select two
principal components from that data? I am sorry if my question is wrong but
please help me.
My second question is, can we use any two parameters like rmsd and Rg for
input in g_sham to probe the stability of complex? Is that valid?
With Regards
Suniba
Sent from my iPhone
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Tsjerk A. Wassenaar, Ph.D.

[sun]

Thank you very much Sir. I get you. Is it good enough to probe the stability of complex by projecting any two variables with free energy? like RMSD and Rg?


Sent from my iPhone

Post by Tsjerk Wassenaar
Hi Suniba,
No, with gmx anaeig you can select -2d, which does a 2D projection onto the
selected eigenvectors. Alternatively, you can combine any two projections
onto eigenvectors, which you get using the option -proj. The quickest way
combined.xvg
You will loose the labels, but that should be fine.
You can combine other variables in a similar manner.
Hope it helps,
Tsjerk

Post by sun
Hello everyone
I am using Gromacs 5.0 for protein-ligand MD. I want to do FEL analysis
for the stability of my pro-lig complex. In a 2015 paper, The group
calculated two principal component, PC1 and PC2 and then prepared an.xvg
file to be used as input for g_sham. My question is, when we use g_anaeig;
we get eigenvec.xvg. from -comp flag. Now how shall one select two
principal components from that data? I am sorry if my question is wrong but
please help me.
My second question is, can we use any two parameters like rmsd and Rg for
input in g_sham to probe the stability of complex? Is that valid?
With Regards
Suniba
Sent from my iPhone
--
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Tsjerk A. Wassenaar, Ph.D.
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[Tsjerk Wassenaar]

Hi Suniba,

No, you will get the stability of configuration in the order parameters you
choose. But you don't know how much conformational freedom you have at each
point. Low RMSD will mean stable, but a fixed point at high RMSD does not.
Also note that the Rg is sort of part of the RMSD, which can be written as
Rg(A)+Rg(B)-2S(A,B), where S is the similarity. So these order parameters
will be correlated.

Cheers,

Tsjerk

Post by sun
Thank you very much Sir. I get you. Is it good enough to probe the
stability of complex by projecting any two variables with free energy? like
RMSD and Rg?
Sent from my iPhone

Post by Tsjerk Wassenaar
Hi Suniba,
No, with gmx anaeig you can select -2d, which does a 2D projection onto

the

Post by Tsjerk Wassenaar
selected eigenvectors. Alternatively, you can combine any two projections
onto eigenvectors, which you get using the option -proj. The quickest way
combined.xvg
You will loose the labels, but that should be fine.
You can combine other variables in a similar manner.
Hope it helps,
Tsjerk

Post by sun
Hello everyone
I am using Gromacs 5.0 for protein-ligand MD. I want to do FEL analysis
for the stability of my pro-lig complex. In a 2015 paper, The group
calculated two principal component, PC1 and PC2 and then prepared an.xvg
file to be used as input for g_sham. My question is, when we use

g_anaeig;

Post by Tsjerk Wassenaar

Post by sun
we get eigenvec.xvg. from -comp flag. Now how shall one select two
principal components from that data? I am sorry if my question is wrong

but

Post by Tsjerk Wassenaar

Post by sun
please help me.
My second question is, can we use any two parameters like rmsd and Rg

for

Post by Tsjerk Wassenaar

Post by sun
input in g_sham to probe the stability of complex? Is that valid?
With Regards
Suniba
Sent from my iPhone
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
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--
Tsjerk A. Wassenaar, Ph.D.
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Post by Tsjerk Wassenaar
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Tsjerk A. Wassenaar, Ph.D.

[sun]

Allright Sir
Thank you very much for clearing the point.
With Regards
Suniba

Sent from my iPhone

Post by Tsjerk Wassenaar
Hi Suniba,
No, you will get the stability of configuration in the order parameters you
choose. But you don't know how much conformational freedom you have at each
point. Low RMSD will mean stable, but a fixed point at high RMSD does not.
Also note that the Rg is sort of part of the RMSD, which can be written as
Rg(A)+Rg(B)-2S(A,B), where S is the similarity. So these order parameters
will be correlated.
Cheers,
Tsjerk

Post by sun
Thank you very much Sir. I get you. Is it good enough to probe the
stability of complex by projecting any two variables with free energy? like
RMSD and Rg?
Sent from my iPhone

Post by Tsjerk Wassenaar
Hi Suniba,
No, with gmx anaeig you can select -2d, which does a 2D projection onto

the

Post by Tsjerk Wassenaar
selected eigenvectors. Alternatively, you can combine any two projections
onto eigenvectors, which you get using the option -proj. The quickest way
combined.xvg
You will loose the labels, but that should be fine.
You can combine other variables in a similar manner.
Hope it helps,
Tsjerk

Post by sun
Hello everyone
I am using Gromacs 5.0 for protein-ligand MD. I want to do FEL analysis
for the stability of my pro-lig complex. In a 2015 paper, The group
calculated two principal component, PC1 and PC2 and then prepared an.xvg
file to be used as input for g_sham. My question is, when we use

g_anaeig;

Post by Tsjerk Wassenaar

Post by sun
we get eigenvec.xvg. from -comp flag. Now how shall one select two
principal components from that data? I am sorry if my question is wrong

but

Post by Tsjerk Wassenaar

Post by sun
please help me.
My second question is, can we use any two parameters like rmsd and Rg

for

Post by Tsjerk Wassenaar

Post by sun
input in g_sham to probe the stability of complex? Is that valid?
With Regards
Suniba
Sent from my iPhone
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
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--
Tsjerk A. Wassenaar, Ph.D.
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Post by Tsjerk Wassenaar
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Tsjerk A. Wassenaar, Ph.D.
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