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

From: Qiang Zhong (zqiang320_at_webmail.hzau.edu.cn)
Date: Mon Aug 13 2007 - 06:53:13 CDT

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!

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