From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Tue Aug 14 2007 - 09:00:20 CDT
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