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
smaric@mail.uh.edu
slladja@gmail.com
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
http://kdi.pnl.gov/bios/baker.stm

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
smaric@mail.uh.edu
slladja@gmail.com
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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