Re: Acetaldehyde Dihedral Parameters

From: L. Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Wed Jun 06 2007 - 11:05:20 CDT

That's strange. If you're using acetaldehyde, such "dihedral"
shouldn't exist (Look at the end of the file you're pointing to).
Instead, there should be an improper to keep such "dihedral"
constrained.

Perhaps you should try to prepare your system again, making sure that
everything looks fine. One more piece of advise: when you use stream
files, you also need to tell psfgen to read a parent file (i.e.,
top_all22_prot.inp).

Cheers,
Michel

2007/6/6, Kevser Göçmen Topal <kevser_at_boun.edu.tr>:
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> Hello,
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> In the stream file "topar_all22_prot-aldehydes.str" dihedral
> parameters for "aldhyde proton-carbonyl carbon-methyl carbon-methyl proton"
> are missing.
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> MD run of my system crashes with error message "FATAL ERROR: CAN'T
> FIND DIHEDRAL PARAMETERS FOR HR1 C CT3 HA" .
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> Does any one have an idea to deal with this problem?
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> Thanks in advance.
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> Best regards,
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> Kevser Göçmen Topal
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