From: Sebastian Stolzenberg (s.stolzenberg_at_gmail.com)
Date: Thu Mar 26 2009 - 19:21:04 CDT
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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