Hi Sladjana –

You could calculate torque forces through finite differencing of the energy:  calculate the energy for several displacements of the rigid domain and then calculate the force through application of a finite difference formula for the derivative.  This should work for a relatively small number of degrees of freedom; e.g., protein domains or the entire protein – rather than every atom or sidechain in the system.

Hope this helps,

__________________________________________________
Nathan Baker
Pacific Northwest National Laboratory
Tel:  509-375-3997
http://kdi.pnl.gov/bios/baker.stm

From: smaric@mail.uh.edu [mailto:smaric@mail.uh.edu]
Sent: Tuesday, August 23, 2011 11:29 AM
To: Baker, Nathan
Cc: Keith Callenberg; APBS mailing_list
Subject: Re: [Apbs-users] Calculate the electrostatic forces for protein

_____________________

Sladjana Maric

Department of Physics

University of Houston

3201 Cullen Blvd

202 HSC, Rm 323D

Houston, TX, 77204-5002

Phone: 713-743-8420

*I can do what I will: I can, if I will, give everything I have to the poor and thus become poor myself — if I will! But I cannot will this, because the opposing motives have much too much power over me for me to be able to. On the other hand, if I had a different character, even to the extent that I were a saint, then I would be able to will it. But then I could not keep from willing it, and hence I would have to do so.*

Dear Dr. Baker

Protein I am working on is rotating, the idea was to use electrostatic forces and try to determine minimum torque necessary for it to rotate. This may be completely wrong approach, but we were thinking it may work since we are focusing only on specific amino acids (active binding sites) on the protein. Hope this is enough information.

Thank you

Sladjana

On Aug 23, 2011, at 12:53 PM, Baker, Nathan wrote:

Hi All –

This is an interesting issue; we haven’t allowed the calculation of forces for surface maps because they are usually decoupled from the atoms for which forces are to be calculated.  However, this isn’t the case for membrane dielectric calculations, so it could be possible to calculate forces in this type of situation – although not necessarily trivial.

Sladjana, can you say a bit more about what you want to learn from these forces?

Thanks,

__________________________________________________
Nathan Baker
Pacific Northwest National Laboratory
Tel:  509-375-3997
http://kdi.pnl.gov/bios/baker.stm

From: smaric@mail.uh.edu [mailto:smaric@mail.uh.edu]
Sent: Tuesday, August 23, 2011 10:10 AM
To: Keith Callenberg
Cc: Baker, Nathan; APBS mailing_list
Subject: Re: [Apbs-users] Calculate the electrostatic forces for protein

Hi,

thank you for pointing out this error. Corrected input file works but it doesn't give the values for Forces, only prints out energy and electrostatic potential. Following message is printed  out "Calculation of forces disabled because surface map is used". Does this mean that I will not be able to do this calculation as long as I am accounting for the influence of membrane on protein? Can you please tell me if there is a way to work around this?

Thank you

Sladjana

_____________________

Sladjana Maric

Department of Physics

University of Houston

3201 Cullen Blvd

202 HSC, Rm 323D

Houston, TX, 77204-5002

Phone: 713-743-8420

*I can do what I will: I can, if I will, give everything I have to the poor and thus become poor myself — if I will! But I cannot will this, because the opposing motives have much too much power over me for me to be able to. On the other hand, if I had a different character, even to the extent that I were a saint, then I would be able to will it. But then I could not keep from willing it, and hence I would have to do so.*

On Aug 23, 2011, at 11:28 AM, Keith Callenberg wrote:

Hi Sladjana,

I'm not sure if this is the only problem, but your syntax has a small bug:
print elecEnergy ref2 - solv2
print elecForce ref2 - solv2
end

You need to have an "end" after the first print statement like this:
print elecEnergy ref2 - solv2 end
print elecForce ref2 - solv2 end

Hope that helps,

Keith

--
Keith M. Callenberg
Carnegie Mellon-University of Pittsburgh Program in Computational Biology
kmc112@{pitt,cmu}.edu
http://www.pitt.edu/~kmc112/

On Tue, Aug 23, 2011 at 12:20 PM, Sladjana Maric <smaric@mail.uh.edu> wrote:

Hello,

Here is the error message. Also I am attaching the input file since error

points to syntax error, and I am having trouble seeing  what is it that I am

doing wrong.

Thank you,

Sladjana

Parsing input file DPL0_2.solv.in...

NOsh:  Deprecated use of ION keyword! Use key-value pairs

NOsh:  Deprecated use of ION keyword! Use key-value pairs

NOsh:  Deprecated use of ION keyword! Use key-value pairs

NOsh:  Deprecated use of ION keyword! Use key-value pairs

NOsh:  Deprecated use of ION keyword! Use key-value pairs

NOsh:  Deprecated use of ION keyword! Use key-value pairs

NOsh:  Deprecated use of ION keyword! Use key-value pairs

NOsh:  Deprecated use of ION keyword! Use key-value pairs

NOsh:  Deprecated use of ION keyword! Use key-value pairs

NOsh:  Deprecated use of ION keyword! Use key-value pairs

NOsh:  Deprecated use of ION keyword! Use key-value pairs

NOsh:  Deprecated use of ION keyword! Use key-value pairs

NOsh_parsePRINT:  Syntax error in PRINT section while reading print!

Error while parsing input file.

Thank you,

Sladjana

_________________

Sladjana Maric

Department of Physics

University of Houston

3201 Cullen Blvd

202 HSC, Rm 323D

Houston, TX, 77204-5002

Phone: 713-743-8420

*I can do what I will: I can, if I will, give everything I have to the poor

and thus become poor myself — if I will! But I cannot will this, because the

opposing motives have much too much power over me for me to be able to. On

the other hand, if I had a different character, even to the extent that I

were a saint, then I would be able to will it. But then I could not keep

from willing it, and hence I would have to do so.*

On Aug 22, 2011, at 9:14 PM, Baker, Nathan wrote:

Hello –

Please send us the error messages you are receiving.

Thanks,

__________________________________________________

Nathan Baker

Pacific Northwest National Laboratory

Tel:  509-375-3997

From: Sladjana Maric [mailto:smaric@mail.uh.edu]

Sent: Monday, August 22, 2011 10:12 AM

To: APBS mailing_list

Subject: [Apbs-users] Calculate the electrostatic forces for protein

Dear APBS users,

I am successfully using the APBS to calculate electrostatic potential for

the protein by introducing the influence of the membrane and heterogeneous

dielectric environment. Now I am trying to calculate the values of the

electrostatic Forces by using calcforce comps, but apbs will not run at all.

Can you please tell me if there is some rule how this keyword should be used

for this kind of calculations. I tried to use it same way the pot and

atompot keywords are used but all attempts failed.

When testing the force calculations on protein without membrane, it seems to

be forking ok.

Sincerely,

Sladjana

_____________________

Sladjana Maric

Department of Physics

University of Houston

3201 Cullen Blvd

202 HSC, Rm 323D

Houston, TX, 77204-5002

Phone: 713-743-8420

*I can do what I will: I can, if I will, give everything I have to the poor

and thus become poor myself — if I will! But I cannot will this, because the

opposing motives have much too much power over me for me to be able to. On

the other hand, if I had a different character, even to the extent that I

were a saint, then I would be able to will it. But then I could not keep

from willing it, and hence I would have to do so.*

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