Re: Error in PSF gen

From: Vibhor Agrawal (vibhora_at_g.clemson.edu)
Date: Tue Jun 18 2013 - 22:36:32 CDT

Hello ivana
As you suggested I tried using command last none
But there is all same error
Also one think I noticed by using the command guesscoord coordinate are
added .I was going through the psfgen tutorial and they made a point in
there by stating any error in the last and first of the capping is normal.

What do you think ...??? Please do let me know

Thanks
VIBHOR
 On Jun 17, 2013 3:40 PM, "Ivana" <stankoviciv_at_gmail.com> wrote:

> Hello, Vibhor!
>
> These are some things I had to deal with:
> 1) you have to avoid automatic addition of hydrogen atoms at the end of a
> sequence.
> segment $S {pdb $S.pdb
> first (or last) none
> first ACP
> last CT1
> }}
>
> 2) I had some problem with PRES CT2 in the topology file
> top_all27_prot_na.inp.
> I couldn't manage to solve it, so I had edited a bit.
> PRES CT2 0.00 ! amidated C-terminus
> GROUP ! use in generate statement
> ATOM C CC 0.55 !
> ATOM O O -0.55 ! |
> GROUP ! O=C
> ATOM NT NH2 -0.62 ! |
> ATOM HT1 H 0.32 ! NT
> ATOM HT2 H 0.30 ! / \
> DELETE ATOM OT1 (I have added)
> DELETE ATOM OT2 (I have added)
> BOND C NT C O (I have added) ! HT1 HT2
> BOND NT HT1 NT HT2 !
> DIHE CA C NT HT2 ! (HT1 is cis to O)
> IMPR C NT CA O C CA NT O
> IMPR NT C HT1 HT2 NT C HT2 HT1
> DONOR HT1 NT
> DONOR HT2 NT
> IC N CA C O 0.0000 0.0000 180.0000 0.0000 0.0000
> IC NT CA *C O 0.0000 0.0000 180.0000 0.0000 0.0000
> IC CA C NT HT1 0.0000 0.0000 180.0000 0.0000 0.0000
> IC HT1 C *NT HT2 0.0000 0.0000 180.0000 0.0000 0.0000
>
> I hope something of this helps.
> Regards, Ivana
>
>
> On 17 June 2013 13:48, Vibhor Agrawal <vibhora_at_g.clemson.edu> wrote:
>
>> .Please help any help will be appreciated
>>
>> Hello all I was creating a psf for my protein and have capped it with the
>> ACP and CT1.
>> When the segment is prepared its giving me following error which I
>> haven't seen before .Please help.
>>
>> psfgen) building segment CB1
>> psfgen) reading residues from pdb file cb1.pdb
>> psfgen) extracted 301 residues from pdb file
>> psfgen) setting patch for first residue to ACP
>> psfgen) setting patch for last residue to CT1
>> psfgen) Info: generating structure...psfgen) Info: skipping improper
>> N-C-CA-CD at beginning of segment.
>> psfgen) Info: skipping conformation C-N-CA-C at beginning of segment.
>> psfgen) Info: skipping conformation C-CA-N-CD at beginning of segment.
>> psfgen) ERROR: Missing atoms for bond C(0) N(1) in residue CYS:300
>> psfgen) ERROR: Missing atoms for improper C(0) CA(0) N(1) O(0)
>> in residue CYS:300
>> psfgen) Warning: missing atoms for conformation CYS CA-C-N-CA; skipping.
>> psfgen) Warning: missing atoms for conformation CYS N-CA-C-O; skipping.
>> psfgen) Warning: missing atoms for conformation CYS N-CA-C-N; skipping.
>> segment complete.
>>
>> below is code which I used:
>>
>> package require psfgen
>> topology ./../topology/top_all27_prot_lipid.rtf
>> pdbalias atom CYS HG HG1
>> pdbalias residue PLM PALM
>> pdbalias residue HOH TIP3
>> pdbalias atom HOH O OH2
>> pdbalias atom ILE CD1 CD
>> pdbalias residue HIS HSE
>> foreach S {cb1} {
>> segment $S {pdb $S.pdb
>> first ACP
>> last CT1
>> }}
>> coordpdb cb1.pdb $S
>> guesscoord
>> writepsf cb1.psf
>>
>> Thanks
>> Vibhor
>>
>>
>

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