Re: Re: about psfgen

From: Ramya Gamini (ramyabhargavi_at_gmail.com)
Date: Sat Jul 04 2009 - 14:43:53 CDT

Oops ! it was 17 11 indeed. Sorry, I was editing the psf and mistook the
original line for 'my' correction.and, the ACE is a CH3CO group added to
have uncharged N terminus, if that was what you needed.
Ramya

2009/7/4 Ramya Gamini <ramyabhargavi_at_gmail.com>

> hi Emilia
> In your psf file, for the first residue, one bond in the side chain for ILE
> is wrong
> there must be a bond between 17 11
> and not 17 13
>
> 221 !NBOND: bonds
> 1 2 1 3 1 4 5 1
> 5 7 6 5 7 8 7 9
> 9 10 11 9 11 12 13 11
> 13 14 13 15 13 16 17 11
>
> You can draw the structure for ILE to determine for yourself. The
> acetylated N terminus (ACE) looks fine to me.
> best,
> Ramya
>
> 2009/7/4 emilia.l.wu <emilia.l.wu_at_gmail.com>
>
> Hi,
>>
>> Thank you for your reply, but the structure of the patched residues (res2
>> and res12) are fine,
>> it is the first residue ACE has the structure problem.
>> I can not attached my psf and pdb file here, I do not know why.
>>
>>
>> Emilia
>>
>> ------------------------------
>> emilia.l.wu
>> 2009-07-04
>> ------------------------------
>> *发件人:* Ramya Gamini
>> *发送时间:* 2009-07-04 09:40:48
>> *收件人:* emilia.l.wu
>> *抄送:* namd-l
>> *主题:* Re: namd-l: about psfgen
>>
>> hi! On including new patches like you have in here- DISU, you must then
>> include a line
>> regenerate angles dihedrals
>>
>> for reference:
>> http://www.ks.uiuc.edu/Research/vmd/plugins/psfgen/ug.pdf
>>
>> hope it helps
>> Ramya
>>
>> On Sat, Jul 4, 2009 at 8:59 AM, emilia.l.wu <emilia.l.wu_at_gmail.com>wrote:
>>
>>> Hi all,
>>>
>>> I use? the psfgen script below to read a pdb file, guess some coordinates
>>> for missing atoms and get another pdb and corresponding
>>> psf file. but I notice if I use vmd -psf prod.psf -pdb prod.pdb to see
>>> the structure, It is obvious that there is some problem of the bond of
>>> ILE1, some bonds are broken, and if I use vmd -pdb prod.pdb to open it,
>>> it looks good. so it should be the problem of the psf file.
>>> cound anyone tell me what 's the problem of the script.
>>>
>>>
>>>
>>> # PSFGEN script to generate PSF from split up PDB file
>>> package require psfgen
>>>
>>> topology "top_mod.rtf"
>>>
>>>
>>> segment PROD {
>>> ?first ACE
>>> ?last CT2
>>> ?pdb m1_prod_ADTaddH.pdb_charmm
>>> }
>>> pdbalias atom ILE CD1 CD
>>> coordpdb m1_prod_ADTaddH.pdb_charmm PROD
>>>
>>> guesscoord
>>>
>>> patch DISU PROD:2 PROD:12
>>>
>>>
>>> writepdb prod.pdb
>>> writepsf prod.psf
>>>
>>> quit
>>>
>>> #ENDMOL
>>>
>>>
>>
>

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