RE: trying to generate a peptide

From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Wed Oct 26 2005 - 09:39:56 CDT

You're getting the "unknown residue type ACE" error because you have a
residue named ACE in your PDB file. You need to make those atoms part of
the adjacent residue (change resname and resid), or just delete them.

-Jim

On Wed, 26 Oct 2005, Richard Wood wrote:

> Well, if you add up the atoms of the sequence, using
> NAMD/psfgen you'd get 152 atoms I believe. My pdb
> file has 150 (including hydrogens).
>
> The program that I used to build the peptide before
> defines NMe as NH-CH3, or six atoms, and not CO-NH-CH3
> (i.e, CT3), which is 8.
>
> Regardless of this, the output I get tells me "unknown
> residue type ACE" or "unknown residue type CT3".
>
> So it still doesn't work.
>
> here's my input:
>
> topology top_all22_prot.inp
>
> segment test { pdb VII-87-B.ent
> first ACE
> last CT3
> }
>
> coordpdb VII-87-B.ent test
>
> guesscoord
>
> writepdb 787B.pdb
> writepsf 787B.psf
> exit
>
> And here's the output...
>
> Created by CHARMM version 22 1
> building segment TEST
> reading residues from pdb file VII-87-B.ent
> extracted 8 residues from pdb file
> setting patch for first residue to ACE
> setting patch for last residue to CT3
> Info: generating structure...
> unknown residue type ACE
>
> Richard
>
> --- Michel Espinoza-Fonseca <mef_at_ddt.biochem.umn.edu>
> wrote:
>
>> those are both residues and patches, and usually you
>> use them the way I wrote you before... I'm not very
>> clear on what you want to get (NME and CT3 are the
>> same thing!). Remember that you're patching the
>> termini, so you'll have a CO tail + the
>> N-metylamide.
>>
>> If you think that this is not clear enough, take a
>> look to the topology file. After the "standard"
>> residues, you'll find the respective patches et al.
>>
>> Michel
>>
>> ________________________________
>>
>> From: owner-namd-l_at_ks.uiuc.edu on behalf of Richard
>> Wood
>> Sent: Wed 10/26/2005 7:34 AM
>> To: namd-l_at_ks.uiuc.edu
>> Subject: RE: namd-l: trying to generate a peptide
>>
>>
>>
>>
>> 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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>>>
>>>
>>
>>
>>
>>
>> __________________________________
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>>
>
>
>
>
>
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