From: Ivana (stankoviciv_at_gmail.com)
Date: Mon Jun 17 2013 - 14:39:00 CDT
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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