From: Qiang Zhong (zqiang320_at_webmail.hzau.edu.cn)
Date: Tue Aug 14 2007 - 19:07:24 CDT
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?
在您的来信中曾经提到:
>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 - 15:45:05 CST