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

[Keith C. <km...@pi...>]

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 <sm...@ma...> 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
> sm...@ma...
> sl...@gm...
> 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:sm...@ma...]
> 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
> sm...@ma...
> sl...@gm...
> 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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