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Protonated valine -theata.parm CT1-CT1-CD needed
#30401 07/19/12 04:28 PM
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prakash Offline OP
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I attempted protonated valine using
PRES CNEU command, top_all22_prot.inp, This builds psf/pdb of protonated valine with vmd.

during the minimization, I ended up following errors,
because my par_all22-prot.inp is missing following angle parameters.

UNABLE TO FIND ANGLE PARAMETERS FOR CD CT1 CT1 (ATOMS 590 588 582)

which particular would be an optimal for this run.

appreciate your help.

thanks

Re: Protonated valine -theata.parm CT1-CT1-CD needed
prakash #30402 07/19/12 05:20 PM
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rmv Online Content
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I wasn't aware that CHARMM could read a PSF generated with VMD.

The angle parameters for CT1-CT2-CD, CT2-CT1-CD, and CT2-CT2-CD are all the same, so you could probably safely assume transferability, and add CT1-CT1-CD using the same values for Ktheta and THETA. Note that it's possible some DIHEdral terms may be missing once you fix the missing ANGLE term.

The CNEU patch is a relatively recent addition, and was apparently not tested on all 20 amino acids.


Rick Venable
computational chemist

Re: Protonated valine -theata.parm CT1-CT1-CD needed
prakash #30406 07/19/12 07:26 PM
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prakash Offline OP
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thank you, works fine


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