Re: Hoe to create psf file of C-terminous of protein?

From: Qiang Zhong (zqiang320_at_webmail.hzau.edu.cn)
Date: Wed Aug 15 2007 - 02:48:53 CDT

Thank you very much! your method work well! I have solved this problem as you
say.

在您的来信中曾经提到:
>From: JC Gumbart <gumbart_at_ks.uiuc.edu>
>Reply-To:
>To: "Qiang Zhong" <zqiang320_at_webmail.hzau.edu.cn>
>Subject: Re: namd-l: Hoe to create psf file of C-terminous of protein?
>Date:Tue, 14 Aug 2007 19:49:33 -0500
>
>You have to make separate pdbs for each chain in your system. When
> you say the chain after ASN, do you mean another protein? ATP? In
> any case, write out separate pdbs for each of these and then use
> multiple segment and coordpdb commands in your script to generate the
> psf.
>
> i.e.
>
> segment A {pdb A.pdb
> ..
> }
> coordpdb A.pdb A
>
> segment B {pdb B.pdb
> ..
> }
> coordpdb B.pdb B
>
> On Aug 14, 2007, at 7:07 PM, Qiang Zhong wrote:
>
> > Thank you very much! I have change .pgn as you say, but error is
> > still there,
> > Then I delete the chain after ASN, Then I find it is correct. So I
> > want to know
> > whether there are another method to solve it?
> >
> >
> > 在您的来信中曾 提到:
> >> From: Peter Freddolino <petefred_at_ks.uiuc.edu>
> >> Reply-To:
> >> To: Qiang Zhong <zqiang320_at_webmail.hzau.edu.cn>
> >> Subject: Re: namd-l: Hoe to create psf file of C-terminous of
> >> protein?
> >> Date:Tue, 14 Aug 2007 09:00:20 -0500
> >>
> >> You're running across two issues:
> >> -You didn't specify that a C terminal patch should be applied. You
> >> either need to have automatic patching defined in your topology
> >> file, or
> >> define the segment as, eg,
> >>
> >> segment BH {
> >> pdb XXX_ATP.pdb
> >> first NTER
> >> last CTER
> >> }
> >>
> >>
> >> to apply N-terminal and C-terminal patches
> >>
> >> -The warnings you got are likely because your input pdb doesn't
> >> follow
> >> charmm naming conventions: the carbonyl oxygen on the last residue is
> >> named OXT, not O. You either need to rename it or alias it.
> >>
> >> Peter
> >>
> >>
> >> Qiang Zhong wrote:
> >>> Dear NAMD Users:
> >>> I have a complex of protein and ATP, when I create psf
> >>> file of
> > complex,
> >>> I got error message:
> >>>
> >>> ERROR: Missing atoms for bond C(0) N(1) in residue ASN:309
> >>> ERROR: Missing atoms for improper C(0) CA(0) N(1) O(0)
> >>> in residue ASN:309
> >>> ERROR: Missing atoms for cross-term C(-1) N(0) CA(0) C(0) N(0) CA
> >>> (0) C(0)
> > N(1)
> >>> in residue ASN:309
> >>>
> >>> where ASN is C-terminous residue of protein,The pdb file of ASN is:
> >>>
> >>> ATOM 2391 N ASN B 309 -25.381 -30.889 6.595 1.00 68.77
> > N
> >>>
> >>> ATOM 2392 CA ASN B 309 -26.117 -30.619 5.364 1.00 70.45
> > C
> >>>
> >>> ATOM 2393 C ASN B 309 -27.266 -29.640 5.606 1.00 71.44
> > C
> >>>
> >>> ATOM 2394 CB ASN B 309 -26.707 -31.905 4.757 1.00 70.80
> > C
> >>>
> >>> ATOM 2395 CG ASN B 309 -25.639 -32.782 4.129 1.00 71.07
> > C
> >>>
> >>> ATOM 2396 OD1 ASN B 309 -25.211 -32.577 3.000 1.00 70.80
> > O
> >>>
> >>> ATOM 2397 ND2 ASN B 309 -25.236 -33.789 4.922 1.00 70.60
> > N
> >>>
> >>> ATOM 2398 OXT ASN B 309 -27.900 -29.717 6.659 1.00 0.00
> > O
> >>>
> >>> The output ASN in the output pdb is:
> >>> ATOM 4731 N ASN B 309 -25.381 -30.889 6.595 1.00
> >>> 0.00 BH
> > N
> >>> ATOM 4732 HN ASN B 309 -25.920 -30.790 7.430 0.00
> >>> 0.00 BH
> > H
> >>> ATOM 4733 CA ASN B 309 -26.117 -30.619 5.364 1.00
> >>> 0.00 BH
> > C
> >>> ATOM 4734 HA ASN B 309 -25.410 -30.137 4.697 0.00
> >>> 0.00 BH
> > H
> >>> ATOM 4735 CB ASN B 309 -26.707 -31.905 4.757 1.00
> >>> 0.00 BH
> > C
> >>> ATOM 4736 HB1 ASN B 309 -27.192 -32.477 5.578 0.00
> >>> 0.00 BH
> > H
> >>> ATOM 4737 HB2 ASN B 309 -27.493 -31.656 4.015 0.00
> >>> 0.00 BH
> > H
> >>> ATOM 4738 CG ASN B 309 -25.639 -32.782 4.129 1.00
> >>> 0.00 BH
> > C
> >>> ATOM 4739 OD1 ASN B 309 -25.211 -32.577 3.000 1.00
> >>> 0.00 BH
> > O
> >>> ATOM 4740 ND2 ASN B 309 -25.236 -33.789 4.922 1.00
> >>> 0.00 BH
> > N
> >>> ATOM 4741 HD21 ASN B 309 -24.527 -34.394 4.569 0.00
> >>> 0.00 BH
> > H
> >>> ATOM 4742 HD22 ASN B 309 -25.622 -33.890 5.834 0.00
> >>> 0.00 BH
> > H
> >>> ATOM 4743 C ASN B 309 -27.266 -29.640 5.606 1.00
> >>> 0.00 BH
> > C
> >>> ATOM 4744 O ASN B 309 -26.897 -28.712 5.658 0.00
> >>> 0.00 BH
> > O
> >>>
> >>> I know it is not correct, because it is not realy C-terminous style.
> >>>
> >>> In my pgn file:
> >>>
> >>> package require psfgen
> >>>
> >>> topology top_all27_prot_na_ppi_thp.inp
> >>>
> >>> pdbalias residue HIS HSE
> >>>
> >>> pdbalias atom ILE CD1 CD
> >>>
> >>> segment BH {pdb XXX_ATP.pdb}
> >>>
> >>> coordpdb XXX_ATP.pdb BH
> >>>
> >>> guesscoord
> >>>
> >>> writepdb XXXATP.pdb
> >>>
> >>> writepsf XXXATP.psf
> >>>
> >>> Could somebody tell me how to solve this problem? Thank you very
> >>> much!
> >>>
> >>>
> >>
> >
>
>
>

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:46:47 CST