Re: paramter

From: snoze pa (snoze.pa_at_gmail.com)
Date: Fri Jun 13 2008 - 10:37:55 CDT

Thanks JC, I fixed the problem and its working now.

On Thu, Jun 12, 2008 at 7:53 PM, JC Gumbart <gumbart_at_ks.uiuc.edu> wrote:
> hmm...maybe try using "pdbalias residue SEP SER" ? Otherwise, I'm not sure
> what could be going on.
>
> As a quick and dirty alternative, you could just manually edit your input
> pdb.
>
> JC
>
> On Jun 12, 2008, at 4:16 PM, snoze pa wrote:
>
>> 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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