Re: paramter

From: snoze pa (snoze.pa_at_gmail.com)
Date: Thu Jun 12 2008 - 16:16:21 CDT

Hi JC, I am using SP2 patch and getting following message:

Info: segment complete.
reading coordinates from pdb file 1T29B.pdb for segment B
Warning: failed to set coordinate for atom P SEP:6 B
Warning: failed to set coordinate for atom O1P SEP:6 B
Warning: failed to set coordinate for atom O2P SEP:6 B
Warning: failed to set coordinate for atom O3P SEP:6 B
applying patch SP2 to 1 residues
Info: guessing coordinates for 102 atoms (5 non-hydrogen)
Warning: poorly guessed coordinates for 9 atoms (5 non-hydrogen):
Warning: poorly guessed coordinate for atom HT1 ILE:1 B
Warning: poorly guessed coordinate for atom HT2 ILE:1 B
Warning: poorly guessed coordinate for atom HT3 ILE:1 B
Warning: poorly guessed coordinate for atom P SER:6 B
Warning: poorly guessed coordinate for atom O1P SER:6 B
Warning: poorly guessed coordinate for atom O2P SER:6 B
Warning: poorly guessed coordinate for atom OT SER:6 B
Warning: poorly guessed coordinate for atom HG2 PRO:7 B
Warning: poorly guessed coordinate for atom OT2 GLN:12 B
Info: writing psf file test_psfgen_1.psf

somehow it is not patching the residue SEP (which i did using alias
residue SEP SER)

Thank you
s

On Wed, Jun 11, 2008 at 9:08 PM, JC Gumbart <gumbart_at_ks.uiuc.edu> wrote:
> You'll find it in the full charmm parameter set here:
> http://mackerell.umaryland.edu/CHARMM_ff_params.html
>
> After untaring it, look in stream/toppar_prot_na_all.str .
>
>
> On Jun 11, 2008, at 5:44 PM, snoze pa wrote:
>
>> Hi All,
>> I am looking parameter for phosphorylated ser residue in namd2. Any help?
>> Thanks in advance
>> s
>
>

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