Re: FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR NH3 HC NH3

From: Chris Harrison (charris5_at_gmail.com)
Date: Sun Jun 21 2009 - 19:11:54 CDT

VMD atom numbers are "0 based; start from 0" while those in the pdb and NAMD
are "1 based". If you use "serial 2314" this should result in selection of
the Nitrogen you desire. The usage of "serial XXX" is akin to using a "1
based" indexing in VMD. If you use "index 2314" this should result in
selection of the atom that will be listed as 2315 in the pdb and within
NAMD. The selection "index XXX" in VMD uses the default "0 based" indexing
in VMD.

Chris

--
Chris Harrison, Ph.D.
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
char_at_ks.uiuc.edu                            Voice: 217-244-1733
http://www.ks.uiuc.edu/~char               Fax: 217-244-6078
On Sun, Jun 21, 2009 at 5:22 PM, gurunath katagi <gurukatagi_at_gmail.com>wrote:
> Hello,
> as you pointed out, there are incorrect bonds and angles, which happen to
> be at the atoms 2314 (N).
> the bond between 2314-2315, 2314-2316,2314-2317 has repeated twice. a part
> of the pdb and psf file has been pasted here:
>
> ATOM   2313  O2D HEMEB 147       9.169  -8.132  25.625  1.00  0.00
> K    O
> *ATOM   2314  N   GGL E   1      -1.790  -2.988  18.399  1.00  0.00
> E    N *
> ATOM   2315  HT1 GGL E   1      -2.114  -3.338  17.520  0.00  0.00
> E    H
> ATOM   2316  HT2 GGL E   1      -0.822  -2.746  18.334  0.00  0.00
> E    H
> ATOM   2317  HT3 GGL E   1      -2.325  -2.186  18.664  0.00  0.00
> E    H
> ATOM   2318  CA  GGL E   1      -1.992  -4.264  19.648  1.00  0.00
> E    C
> ATOM   2319  HA  GGL E   1      -2.956  -4.450  20.106  0.00  0.00
> E    H
> ATOM   2320  C   GGL E   1      -1.330  -2.940  20.412  1.00  0.00
> E    C
> ATOM   2321  OT1 GGL E   1      -2.687  -2.214  20.777  1.00  0.00
> E    O
> ATOM   2322  OT2 GGL E   1      -0.482  -1.986  20.209  1.00  0.00
> E    O
> ATOM   2323  CB  GGL E   1      -2.596  -4.826  18.364  1.00  0.00
> E    C
> ATOM   2324  HB1 GGL E   1      -3.042  -3.981  17.791  0.00  0.00
> E    H
> ATOM   2325  HB2 GGL E   1      -1.790  -5.241  17.718  0.00  0.00
> E    H
> ATOM   2326  CG  GGL E   1      -3.654  -5.870  18.608  1.00  0.00
> E    C
> ATOM   2327  HG1 GGL E   1      -3.231  -6.689  19.218  0.00  0.00
> E    H
> ATOM   2328  HG2 GGL E   1      -4.526  -5.436  19.135  0.00  0.00
> E    H
> ATOM   2329  CD  GGL E   1      -4.140  -6.519  17.338  1.00  0.00
> E    C
> ATOM   2330  O   GGL E   1      -3.553  -6.345  16.265  1.00  0.00
> E    O
> ATOM   2331  SG  CYS E   2      -3.622  -9.735  16.464  1.00  0.00
> E    S
> ATOM   2332  CB  CYS E   2      -5.417  -9.444  16.361  1.00  0.00
> E    C
> ATOM   2333  N   CYS E   2      -5.234  -7.265  17.467  1.00  0.00
> E    N
> ATOM   2334  HN  CYS E   2      -5.545  -7.559  18.369  0.00  0.00
> E    H
> ATOM   2335  CA  CYS E   2      -5.845  -7.971  16.351  1.00  0.00
> E    C
> ATOM   2336  HA  CYS E   2      -5.567  -7.453  15.441  0.00  0.00
> E    H
> ATOM   2337  HB1 CYS E   2      -5.887  -9.918  17.252  0.00  0.00
> E    H
> ATOM   2338  HB2 CYS E   2      -5.841  -9.966  15.475  0.00  0.00
> E    H
> ATOM   2339  C   CYS E   2      -7.365  -7.879  16.493  1.00  0.00
> E    C
> ATOM   2340  O   CYS E   2      -7.898  -7.939  17.605  1.00  0.00
> E    O
> ATOM   2341  C   GLY E   3      -9.981  -6.251  15.014  1.00  0.00
> E    C
> ATOM   2342  OT1 GLY E   3     -11.138  -6.128  14.558  1.00  0.00
> E    O
> ATOM   2343  OT2 GLY E   3      -9.194  -5.290  15.152  1.00  0.00
> E    O
> ATOM   2344  N   GLY E   3      -8.053  -7.733  15.368  1.00  0.00
> E    N
> ATOM   2345  HN  GLY E   3      -7.630  -7.681  14.464  0.00  0.00
> E    H
> ATOM   2346  CA  GLY E   3      -9.499  -7.638  15.390  1.00  0.00
> E    C
> ATOM   2347  HA1 GLY E   3      -9.818  -7.840  16.403  0.00  0.00
> E    H
> ATOM   2348  HA2 GLY E   3      -9.882  -8.334  14.656  0.00  0.00
> E    H
>
>
> bonds:(repeated twice):
> 2308    2310    2311    2312    2311    2313    2315    2314
> *2315    2314    2316    2314    2316    2314    2317    2314
> 2317    2314    2318    2314*    2318    2319    2318    2320
>
> angles:
>  2314    2317    2314    2314    2316    2314    2314    2315    2314
>
> this actually represents NH3-HC-NH3 bond which is not desired(or not all
> there according to pdb file or strcuture)
>
> One more thing i have observed is that, when i load the psf and pdb file :
> if i make representation like 'index 2314', it should point to nitrogen
> atom(N), but instead it points to one of the three hydrogens(HT).
> what is the reason that, there is repetition in the bond order and angle
> terms.
>
> how do i come out of this error? . If i remove the some of the bond terms
> and alngle parameters from psf file and run it, i get the following error.
> ------------- Processor 0 Exiting: Called CmiAbort ------------
> Reason: FATAL ERROR: BOND INDEX 4339 GREATER THAN NATOM 2348 IN BOND # 2386
> IN PSF FILE
>
> Charm++ fatal error:
> FATAL ERROR: BOND INDEX 4339 GREATER THAN NATOM 2348 IN BOND # 2386 IN PSF
> FILE
>
> and as such, i think , there is no parameter file available for a bond like
> NH3-HC -NH3 unless it is H-bond. Since in my case it it not a hydrogen bond,
> i want to remove it.
>
> Is there any way that i can rectify this.? , or can i get the following
> protein(pdb file) minimized.
> the pdb file is globin.pdb
> the script for the psf file creation is deoxy_psf.tcl
> for minimization, minimize.conf
> Please look into this and reply.
>
> Thanks and regards,
> Gurunath
>
>
>
>
> On Sun, Jun 21, 2009 at 11:24 PM, Axel Kohlmeyer <
> akohlmey_at_cmm.chem.upenn.edu> wrote:
>
>> On Sat, 2009-06-20 at 23:29 +0530, gurunath katagi wrote:
>> > Hello everyone,
>> > I have a PDB file glob1.pdb..(file generated by combining two pdb
>> > files). I have created the psf file using the script .
>> > I need to minimize the structure using namd.
>> > when I run the file as:
>> > /home/dynamics/NAMD_2.6_Linux-i686/namd2 ghb_minimize.conf >ghb.log ,
>> > the following error is generated:
>> >
>> > ------------- Processor 0 Exiting: Called CmiAbort ------------
>> > Reason: FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR NH3 HC NH3
>>
>> please check your .psf file.
>> this looks as if you have an incorrect angle definition,
>> which could happen, if you have incorrect bonds.
>>
>> cheers,
>>   axel.
>>
>> > Charm++ fatal error:
>> > FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR NH3 HC NH3
>> > Aborted
>> > My question is : whether I have to alter the psf file that i have
>> > got.. or give a parmater file for heme since C-CPB bond is found in
>> > the psf file.
>>
>>
>>
>> >
>> > The files can be downloaded from the following link:
>> >  http://ssl.serc.iisc.ernet.in/~pralay/Pralay%27s%%>
>> > 20Home_files/publication/minimize_hb.tar.gz
>> >
>> > protein.pdb -- the original pdb file
>> > protein_1.pdb -- the pdb file created by psfgen
>> > protein_1.psf -- the psf file creted after psfgen
>> > deoxy_psf.tcl --  script for psf file cretation
>> > minimize.conf -- config file for minimization
>> >
>> > The topology and parameter file that i have used include --
>> > top_all27_prot_lipid.inp , toppar_all22_prot_heme.str,
>> > top_all27_prot_lipid_gsh.inp and par_all27_prot_lipid.inp
>> >
>> > Can any body please look into this.and give some suggestions.
>> >
>> >
>> > --
>> > Gurunath M Katagi
>> > M.Sc (engg) Research student
>> > Supercomputer Education and Research Centre
>> > Indian Institute Of Science
>> > Bangalore
>>
>> --
>> =======================================================================
>> Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
>>   Center for Molecular Modeling   --   University of Pennsylvania
>> Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
>> tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
>> =======================================================================
>> If you make something idiot-proof, the universe creates a better idiot.
>>
>>
>
>
> --
> Gurunath M Katagi
> M.Sc (engg) Research student
> Supercomputer Education and Research Centre
> Indian Institute Of Science
> Bangalore
>

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