Re: Error in PSF gen

From: Ivana (stankoviciv_at_gmail.com)
Date: Wed Jun 19 2013 - 10:14:36 CDT

It looks like the problem is not the ACP/CT1 patch.
Can you send your .pdb, please?

On 19 June 2013 00:36, Vibhor Agrawal <vibhora_at_g.clemson.edu> wrote:

> 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
>>>
>>>
>>

This archive was generated by hypermail 2.1.6 : Wed Dec 31 2014 - 23:21:19 CST