[AMBER] Electrostatic potential calculation

From: Sudarshan Debnath <sudarshandebnath.ku.rediffmail.com>
Date: 16 Apr 2012 13:47:57 -0000

Dear Sir,

        Thanks for information. I am a user of Amber11. But I follow the Amber tools12 manual as you suggested. My query is simple- I want to calculate electrostatic potential by pbsa and see the surface in VMD. For a trial I take a small protein molecule made by six amino acids. Using tleap create prmtop and inpcrd for this pdb. Then follow Amber tools11 manual using the following the following input



Sample PB visualization input

&cntrl

ntx=1,

imin=1,

ipb=1,

inp=0

/

&pb

npbverb=1, istrng=0, epsout=80.0, epsin=1.0,

space=1., accept=0.001,

sprob=1.4, cutnb=9,

phiout=1, phiform=2

/

Then use the command



./pbsa –O –i **.in –o **.out –p **.prmtop –c **.inpcrd



The following script is appeared in the terminal box-



Cannot match namelist object name espout

namelist read: missplaced = sign

cannot match namelist object name 0,

cannot match namelist object name espin

namelist read: missplaced = sign



Then **.out file is created. But pbsa.phi.dx is not appeared. Then I follow Amber tools12 manual and use the following input-



Sample PB visualization input

&cntrl

inp=0

/

&pb

npbverb=1, space=1., sasopt=2,

phiout=1, phiform=2

/



The following script is appeared in the terminal box after the same commanded is used-



Cannot match namelist object name sasopt

namelist read: missplaced = sign

 

Here also **.out file is created, but pbsa.phi.dx is not appeared. I attached the input, output, prmtop and inpcrd file in this mail. What is mistake that I follow again and again? Please let me know.



With best regards,

Sudarshan.



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Received on Mon Apr 16 2012 - 07:00:02 PDT
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