Re: Re: about psfgen

From: Ramya Gamini (ramyabhargavi_at_gmail.com)
Date: Sat Jul 04 2009 - 14:33:32 CDT

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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