Re: trying to generate a peptide

From: Giovanni Bellesia (giovanni.bellesia_at_ucd.ie)
Date: Wed Oct 26 2005 - 11:27:43 CDT

Hi,
in the topology file you should have a line resembling this one
DEFA FIRS 'name1' LAST 'name2'
where name1 and name2 are the default names for the termini groups

Change it into the following
DEFA FIRS ACE LAST CT3
and try to run your psf generator file without any instruction for the
termini,
i.e., get rid of
> first ACE
> last CT3

let me know if it works

Giovanni

On 26 Oct 2005, at 15:26, 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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