Re: alanine dipeptide: no dihdral energy terms?

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Fri Mar 27 2009 - 14:42:54 CDT

Hi Sebastian,
"X" is a wildcard and indicates that iff no other matching dihedral can
be found (one with the exact names in any of the dihedral entries), the
one containing the wildcards will be used.

Peter

Sebastian Stolzenberg wrote:
> Dear All (Dear Peter),
>
> for the alanine dipeptide, I made some progress and found force
> constants for all but three types of dihdrals (also shown in reverse
> order):
>
> ["HB CT1 CT3 HA ", "HA CT3 CT1 HB "]
> ["HA CT3 CT1 C ", "C CT1 CT3 HA "]
> ["NH1 CT1 CT3 HA ", "HA CT3 CT1 NH1"]
>
> In the parameter files (like in par_all27_prot_na.inp), does "X" act as
> a atom type placeholder?
>
> If yes:
> I could use "X CT1 CT3 X", "NH1 X X H",...
> Can I rely on non-redundancy, i.e. the only way to describe "HB CT1
> CT3 HA " is by "X CT1 CT3 X"?)
>
> If no:
> how else can I find the 3 missing force constants?
>
> Thank you,
> Sebastian
>
>
> Peter Freddolino wrote:
>> Hi Sebastian,
>> could you be more specific about what you expected to see, but didn't?
>> All that I see below are some mangled lines that look like they came
>> from a pdb file. Did you look in the parameter file for the atom *types*
>> (not names) that are in the backbone? I assure you that there are
>> dihedral entries for them...
>>
>> Best,
>> Peter
>>
>> Sebastian Stolzenberg wrote:
>>
>>> Dear All,
>>>
>>> I am a little confused trying to find dihedral force constants for my
>>> alanine dipeptide (see bottom of this e-mail).
>>> I ran simulations with "par_all27_prot_na.inp", but meticulously looking
>>> for atoms along the backbone, I don't find any dihedral entries for it.
>>>
>>> Does anybody know the solution to my mystery?
>>> Thank you,
>>> Best,
>>> Sebastian
>>>
>>>
>>>
>>>
>>> ATOM 1 CAY ALA P 1 12.989 -6.219 -7.507 1.00
>>> 0.00 PEPT ATOM 2 HY1 ALA P 1 12.850 -6.809 -6.576
>>> 1.00 0.00 PEPT ATOM 3 HY2 ALA P 1 14.065 -6.060
>>> -7.736 1.00 0.00 PEPT ATOM 4 HY3 ALA P 1 12.596
>>> -6.978 -8.217 1.00 0.00 PEPT ATOM 5 CY ALA P 1
>>> 12.196 -4.913 -7.519 1.00 0.00 PEPT ATOM 6 OY ALA P
>>> 1 12.278 -4.195 -6.513 1.00 0.00 PEPT ATOM 7 N
>>> ALA P 1 11.355 -4.629 -8.508 1.00 0.00 PEPT ATOM
>>> 8 HN ALA
>>> P 1 11.423 -5.192 -9.327 1.00 0.00 PEPT ATOM 9
>>> CA ALA P 1 10.519 -3.408 -8.519 1.00 0.00 PEPT
>>> ATOM 10 HA ALA P 1 11.150 -2.587 -8.213 1.00
>>> 0.00 PEPT ATOM 11 CB ALA P 1 10.129 -3.154 -9.950
>>> 1.00 0.00 PEPT
>>> ATOM 12 HB1 ALA P 1 10.953 -3.079 -10.692 1.00
>>> 0.00 PEPT ATOM 13 HB2 ALA P 1 9.608 -4.060 -10.328
>>> 1.00 0.00 PEPT ATOM 14 HB3 ALA P 1 9.549 -2.207
>>> -9.937 1.00 0.00 PEPT ATOM 15 C ALA P 1 9.407
>>> -3.423 -7.442 1.00 0.00 PEPT ATOM 16 O ALA P 1
>>> 9.492 -2.936 -6.326 1.00 0.00 PEPT ATOM 17 NT ALA P
>>> 1 8.194 -3.936 -7.766 1.00 0.00 PEPT ATOM 18 HNT
>>> ALA P 1 8.122 -4.379 -8.656 1.00 0.00 PEPT ATOM
>>> 19 CAT ALA
>>> P 1 7.156 -4.023 -6.744 1.00 0.00 PEPT ATOM 20 HT1
>>> ALA P 1 7.251 -3.539 -5.748 1.00 0.00 PEPT ATOM
>>> 21 HT2 ALA P 1 6.277 -3.623 -7.293 1.00 0.00 PEPT
>>> ATOM 22 HT3 ALA P 1 6.830 -5.084 -6.721 1.00
>>> 0.00 PEPT
>>>

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