Re: the problem on segment a ligand in NAMD ?

From: Fangqiang Zhu (fzhu_at_ks.uiuc.edu)
Date: Fri Nov 28 2003 - 00:41:19 CST

Hi,

The problem is due to incorrect format of your PDB file. Please note that PDB
files are column based, and everything must appear in the correct column(s).
In other words, it's not safe to add or remove spaces between data in a PDB
file. You can compare your file to a standard PDB file (e.g., one downloaded
from the Protein Data Bank), and make sure that every field (especially the
resid field) be in the same columns in both files.

Zhu, Fangqiang

yxiong_at_mail.ccnu.edu.cn wrote:

> Dear sir,
> I want to generate pdb and psf file for an enzyme and a ligand. However I get
> the following error information:
> ------------------------------------------------
> % segment lig {pdb lig1.pdb}
> building segment LIG
> reading residues from pdb file lig1.pdb
> extracted 0 residues from pdb file
> Info: generating structure...
> Info: segment complete.
> ------------------------------------------------
> My lig1.pdb is as follows:
> ---------------------------------------------
> HETATM 1 CG EBP 1 50.005 -9.192 29.754 1.00 0.10 C
> HETATM 2 CB EBP 1 48.762 -8.865 28.953 1.00 0.08 C
> HETATM 3 HB1 EBP 1 47.917 -9.487 29.236 1.00 0.29 H
> HETATM 4 HB2 EBP 1 48.923 -8.901 27.880 1.00 0.29 H
> HETATM 5 P1 EBP 1 48.245 -7.381 29.251 1.00 0.48 P
> HETATM 6 O3 EBP 1 48.250 -6.595 27.988 1.00 -0.21 O
> HETATM 7 O1 EBP 1 49.211 -6.725 30.341 1.00 -0.28 O
> HETATM 8 C1 EBP 1 49.448 -7.216 31.667 1.00 0.06 C
> HETATM 9 H11 EBP 1 49.872 -8.233 31.627 1.00 0.06 H
> HETATM 10 H12 EBP 1 50.161 -6.552 32.182 1.00 0.06 H
> HETATM 11 C3 EBP 1 48.099 -7.236 32.423 1.00 -0.04 C
> HETATM 12 H31 EBP 1 48.240 -7.600 33.453 1.00 0.03 H
> HETATM 13 H32 EBP 1 47.675 -6.220 32.459 1.00 0.03 H
> HETATM 14 H33 EBP 1 47.389 -7.898 31.904 1.00 0.03 H
> HETATM 15 O2 EBP 1 46.761 -7.499 29.833 1.00 -0.28 O
> HETATM 16 C2 EBP 1 45.644 -8.085 29.148 1.00 0.06 C
> HETATM 17 H21 EBP 1 45.490 -7.513 28.219 1.00 0.06 H
> HETATM 18 H22 EBP 1 44.737 -7.992 29.769 1.00 0.06 H
> HETATM 19 C4 EBP 1 45.910 -9.571 28.806 1.00 -0.04 C
> HETATM 20 H41 EBP 1 46.807 -9.670 28.176 1.00 0.03 H
> HETATM 21 H42 EBP 1 46.070 -10.151 29.729 1.00 0.03 H
> HETATM 22 H43 EBP 1 45.048 -9.992 28.266 1.00 0.03 H
> HETATM 23 CD1 EBP 1 50.168 -10.464 30.314 1.00 -0.01 C
> HETATM 24 HD1 EBP 1 49.404 -11.225 30.185 1.00 0.07 H
> HETATM 25 CE1 EBP 1 51.315 -10.771 31.052 1.00 -0.06 C
> HETATM 26 HE1 EBP 1 51.427 -11.762 31.481 1.00 0.06 H
> HETATM 27 CZ EBP 1 52.312 -9.809 31.242 1.00 -0.05 C
> HETATM 28 C5 EBP 1 53.577 -10.150 32.040 1.00 -0.04 C
> HETATM 29 H51 EBP 1 53.794 -11.222 31.921 1.00 0.03 H
> HETATM 30 H52 EBP 1 54.438 -9.568 31.680 1.00 0.03 H
> HETATM 31 H53 EBP 1 53.437 -9.931 33.110 1.00 0.03 H
> HETATM 32 CE2 EBP 1 52.143 -8.533 30.696 1.00 -0.06 C
> HETATM 33 HE2 EBP 1 52.904 -7.772 30.848 1.00 0.06 H
> HETATM 34 CD2 EBP 1 50.998 -8.226 29.956 1.00 -0.01 C
> HETATM 35 HD2 EBP 1 50.890 -7.227 29.544 1.00 0.07 H
> CONECT 1 2 23 34
> CONECT 2 1 3 4 5
> CONECT 3 2
> CONECT 4 2
> CONECT 5 2 6 7 15
> CONECT 6 5
> CONECT 7 5 8
> CONECT 8 7 9 10 11
> CONECT 9 8
> CONECT 10 8
> CONECT 11 8 12 13 14
> CONECT 12 11
> CONECT 13 11
> CONECT 14 11
> CONECT 15 5 16
> CONECT 16 15 17 18 19
> CONECT 17 16
> CONECT 18 16
> CONECT 19 16 20 21 22
> CONECT 20 19
> CONECT 21 19
> CONECT 22 19
> CONECT 23 1 24 25
> CONECT 24 23
> CONECT 25 23 26 27
> CONECT 26 25
> CONECT 27 25 28 32
> CONECT 28 27 29 30 31
> CONECT 29 28
> CONECT 30 28
> CONECT 31 28
> CONECT 32 27 33 34
> CONECT 33 32
> CONECT 34 1 32 35
> CONECT 35 34
> MASTER 0 0 0 0 0 0 0 0 35 0 35 0
> END
> ------------------------------------------------
> I have generate the topology for this ligand. I named this ligand as residue
> "EBP". Why did the "segment command" extract 0 residues from pdb file? I have
> signe this ligand as "EBP", why can the command not recognize it?
>
> I am looking forward to your suggestion!

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