Re: the problem on segment a ligand in NAMD ?

From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Fri Nov 28 2003 - 00:30:13 CST

Might it be that you have HETATM labels? If I remember right psfgen
ignores HETATM labels...

Brian

On Fri, 28 Nov 2003, 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!
>
>
>
>

-- 
*****************************************************************
**Brian Bennion, Ph.D.                                         **
**Computational and Systems Biology Division                   **
**Biology and Biotechnology Research Program                   **
**Lawrence Livermore National Laboratory                       **
**P.O. Box 808, L-448    bennion1_at_llnl.gov                     **
**7000 East Avenue       phone: (925) 422-5722                 **
**Livermore, CA  94550   fax:   (925) 424-6605                 **
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