From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Wed Jun 06 2007 - 11:51:57 CDT
Actually... in looking at the topology files, the auto dihedrals is
being pulled in by the parent topology file (top_all22_prot.inp). Michel
(or anyone else), do you happen to know if the auto statement is
supposed to propagate to stream files that are loaded in? If so, that
dihedral *should* be there, and the parameters are just missing. If not,
Kevser, you'll need to include "auto none; auto angles" in the segment
command for generating the acetaldehyde, to avoid making that dihedral:
segment A {
pdb aald.pdb
auto none
auto angles
first none
last none
}
Peter
Peter Freddolino wrote:
> 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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