Re: alanine dipeptide: no dihdral energy terms?

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Mon Mar 23 2009 - 22:45:01 CDT

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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