From: Richard Wood (rwoodphd_at_yahoo.com)
Date: Wed Oct 26 2005 - 07:34:59 CDT
That doesn't work either, because ACE and CT3 are
PRESes and not RESIs.
Besides, CT3 is CO-NH-CH3 and NOT NH-CH3. My peptide
has NH-CH3 at the terminus.
Richard
--- Michel Espinoza-Fonseca <mef_at_ddt.biochem.umn.edu>
wrote:
> Hi,
>
> The actual patch you need to apply is ACE and CT3
> (the first one for acetylated N-terminus, the last
> one for N-Methylamide C terminus).
> Here is an example on how to automatically patch the
> termini of your peptide:
>
> topology toppar/top_all27_prot_na.inp
> segment HPEP { pdb your_file.pdb
> first ACE
> last CT3
> }
> coordpdb your_file.pdb HPEP
> guesscoord
> writepdb your_output_file.pdb
> writepsf your_output_file.psf
>
> And that's all.
>
> Hope it helps,
>
> Michel
>
> ________________________________
>
> From: owner-namd-l_at_ks.uiuc.edu on behalf of Richard
> Wood
> Sent: Tue 10/25/2005 8:07 PM
> To: namd-l_at_ks.uiuc.edu
> Subject: namd-l: trying to generate a peptide
>
>
>
> Hi all,
> Now I'm trying to generate a hexapeptide using a
> previoulsy created pdb file and psfgen.
>
> Here's the sequence of the peptide:
>
> Ace-Arg-Tyr-Tyr-Arg-Trp-Arg-NMe
>
> psfgen tells me there is no such residue as NMe or
> Ace. I'm using top_all22_prot.inp, and there is an a
> PRES ACE present. However, there is NO topology for
> NMe, which is NH-CH3.
>
> The molecule should have 150 atoms. Can anybody
> provide any assistance in generating the "correct"
> residues ACE and NMe? (ACE is CH3-C=O)
>
> Thanks in advance,
> Richard
>
> p.s. I've succeeded in minimizing my protein and now
> I'm running 1020000 steps (1020 ps) of dynamics.
>
>
>
>
>
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