Re: Acetaldehyde Dihedral Parameters

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Wed Jun 06 2007 - 11:19:42 CDT

You may also need to make sure you're *not* using an AUTO DIHEDRALS
directive in psfgen, if the acetaldehyde topology isn't designed to have
one...

Peter

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

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