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