[gmx-users] atomtype problem (was Re: gmx-users Digest, Vol 77, Issue 150)
Justin A. Lemkul
jalemkul at vt.edu
Fri Sep 24 13:57:12 CEST 2010
lloyd riggs wrote:
>
> Dear Users and Justin,
>
> Included below is the origional message and reply. The only error message
> was " Atom type CH2r not found fatal error ".
>
> After looking at all the files though, I realized if I change everything to
> either CH2r or CH2R , it runs. I don't know if it was somones joke on my
Are you saying there's actually a mixture of both CH2r and CH2R in the pdb2gmx
topology? As far as I can tell, all Gromos96 parameter sets (45a3, 53a5, 53a6)
now use CH2r. In past versions of Gromacs, 45a3 used CH2r, but 53a5 and 53a6
used CH2R.
> end, or if it is just a typo in the last release. Basically the nonbonded
> atom files and all the other files had seperate lables at least for me....
>
Sounds like someone was playing with your force field files. Start from a fresh
Gromacs installation and see if that solves your problem. Version 4.5.1 is
internally self-consistent and should have no problems.
-Justin
>> Well, proline isn't aromatic at all...
>
> yeah I know, the terminal C on the ring can be CHR or CH1 , at least the
> definitions are the same...
>
> Origional post:
>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org> Message-ID:
> <4C9A67DE.6060609 at vt.edu> Content-Type: text/plain; charset=UTF-8;
> format=flowed
>
>
> I've gone ahead and changed the subject line to potentially attract the
> attention of others who might help.
>
> lloyd riggs wrote:
>> Dear All,
>>
>> I'm not sure if this is a bug or not. I downloaded and installed the new
>> version of Gromacs, and compiled it fine, and recompiled just mdrun_mpi....
>>
>>
>> The problem I now encounter. U was using 53a6 FF, which worked in the
>> past, although I am partial to all atoms. In Pro residues, the topolog
>> output from grompp lables three of the CH2 in the ring as CH2r. When I
>> then do an EM or MD, gromacs complains that it can not find atom type CH2r.
>> I looked through all the .itp, .rtp and amino acid definitions, and CH2r is
>> there. If I re-lable the topology and .gro file by hand to CHR1 the system
>> works, but the overall geometry is slightly off (if you look at the atom
>> definitions and take into account that prolines are not completly
>> aeromatic, only partially...
>>
>
> Well, proline isn't aromatic at all, but CHR1 will try to force the atoms to
> be planar. None of this should be necessary (nor is it right to do).
>
>> In any case, is this a bug or is there some other problem I missed? I did
>> look at the input .pdb file, and the same nomenclature I used before with
>> the same ff now does not work?
>>
>
> All signs point to the fact that processing of proline should work out of the
> box, so to speak. The CH2r atom type is properly defined in all the
> relevant files. Can you post a bit more detail, like the exact error
> message, snippet from the topology, etc? I haven't had any problem with
> proline-containing proteins with 53a6 in the newest version.
>
> -Justin
>
>> Sincerely
>>
>> Stephan Watkins
>
> Aminoacids.rtp --PRO entry
>
> [ PRO ] [ atoms ] N N 0.00000 0 CA CH1 0.00000 1 CB
> CH2r 0.00000 1 CG CH2r 0.00000 2 CD CH2r 0.00000 2
> C C 0.450 3 O O -0.450 3 [ bonds ] N CA
> gb_21 N CD gb_21 CA CB gb_27 CA C gb_27 CB CG gb_27
> CG CD gb_27 C O gb_5 C +N gb_10 [ angles ] ; ai aj
> ak gromos type -C N CA ga_31 -C N CD ga_31 CA N
> CD ga_21 N CA CB ga_13 N CA C ga_13 CB CA C
> ga_13 CA CB CG ga_13 CB CG CD ga_13 N CD CG
> ga_13 CA C O ga_30 CA C +N ga_19 O C +N
> ga_33 [ impropers ] ; ai aj ak al gromos type N -C CA CD
> gi_1 CA N C CB gi_2 C CA +N O gi_1 [ dihedrals ]
> ; ai aj ak al gromos type -CA -C N CA gd_14 -C
> N CA C gd_39 CA N CD CG gd_39 N CA CB CG
> gd_34 N CA C +N gd_40 CA CB CG CD gd_34 CB CG
> CD N gd_34
>
>
> Atom Definitions---Bonded
>
> O 15.99940 ; carbonyl oxygen (C=O) OM 15.99940 ; carboxyl oxygen
> (CO-) OA 15.99940 ; hydroxyl, sugar or ester oxygen OE 15.99940 ;
> ether or ester oxygen OW 15.99940 ; water oxygen N 14.00670 ;
> peptide nitrogen (N or NH) NT 14.00670 ; terminal nitrogen (NH2) NL
> 14.00670 ; terminal nitrogen (NH3) NR 14.00670 ; aromatic nitrogen
> NZ 14.00670 ; Arg NH (NH2) NE 14.00670 ; Arg NE (NH) C 12.01100 ;
> bare carbon CH0 12.0110 ; bare sp3 carbon, 4 bound heavy atoms CH1
> 13.01900 ; aliphatic or sugar CH-group CH2 14.02700 ; aliphatic or
> sugar CH2-group CH3 15.03500 ; aliphatic CH3-group CH4 16.04300 ;
> methane CH2r 14.02700 ; CH2-group in a ring *************** CR1
> 13.01900 ; aromatic CH-group HC 1.00800 ; hydrogen bound to carbon
> H 1.00800 ; hydrogen not bound to carbon DUM 0.00000 ; dummy
> atom, no idea what the mass should be. PT3-99 S 32.06000 ; sulfur CU1+
> 63.54600 ; copper (charge 1+) CU2+ 63.54600 ; copper (charge 2+) FE
> 55.84700 ; iron (heme) ZN2+ 65.37000 ; zinc (charge 2+) MG2+
> 24.30500 ; magnesium (charge 2+) CA2+ 40.08000 ; calcium (charge 2+)
> P 30.97380 ; phosphor AR 39.94800 ; argon F 18.99840 ; fluor
> (non-ionic) CL 35.45300 ; chlorine (non-ionic) BR 79.90400 ;
> bromine (non-ionic) CMet 15.035 ; CH3-group in methanol (solvent) OMet
> 15.9994 ; oxygen in methanol (solvent) NA+ 22.9898 ; sodium
> (charge 1+) CL- 35.45300 ; chlorine (charge 1-) CChl 12.011 ;
> carbon in chloroform (solvent) CLChl 35.453 ; chloride in chloroform
> (solvent) HChl 1.008 ; hydrogen in chloroform (solvent) SDmso
> 32.06000 ; DMSO Sulphur (solvent) CDmso 15.03500 ; DMSO Carbon
> (solvent) ODmso 15.99940 ; DMSO Oxygen (solvent) CCl4 12.011 ;
> carbon in carbontetrachloride (solvent) CLCl4 35.453 ; chloride in
> carbontetrachloride (solvent) FTFE 18.99840 ; fluor in trifluoroethanol
> CTFE 12.01100 ; carbon in trifluoroethanol CHTFE 14.0270 ;
> CH2-group in trifluoroethanol OTFE 15.99940 ; oxygen in trifluoroethanol
> CUrea 12.01100 ; carbon in urea OUrea 15.99940 ; oxygen in urea
> NUrea 14.00670 ; nitrogen in urea SI 28.08 ; silicon MNH3 0
> ; Dummy mass in rigid tetraedrical NH3 group MW 0 ; Dummy
> mass in rigid tyrosine rings
>
> ffnonbonded atoms----
>
> [ atomtypes ] ;name at.num mass charge ptype c6 c12
> O 8 0.000 0.000 A 0.0022619536 1e-06 OM 8 0.000
> 0.000 A 0.0022619536 7.4149321e-07 OA 8 0.000 0.000 A
> 0.0022619536 1.505529e-06 OE 8 0.000 0.000 A 0.0022619536
> 1.21e-06 OW 8 0.000 0.000 A 0.0026173456 2.634129e-06 N 7
> 0.000 0.000 A 0.0024364096 2.319529e-06 NT 7 0.000 0.000
> A 0.0024364096 5.0625e-06 NL 7 0.000 0.000 A 0.0024364096
> 2.319529e-06 NR 7 0.000 0.000 A 0.0024364096 3.389281e-06 NZ
> 7 0.000 0.000 A 0.0024364096 2.319529e-06 NE 7 0.000
> 0.000 A 0.0024364096 2.319529e-06 C 6 0.000 0.000 A
> 0.0023406244 4.937284e-06 CH0 6 0.000 0.000 A 0.0023970816
> 0.0002053489 CH1 6 0.000 0.000 A 0.00606841 9.70225e-05 CH2
> 6 0.000 0.000 A 0.0074684164 3.3965584e-05 CH3 6 0.000
> 0.000 A 0.0096138025 2.6646244e-05 CH4 6 0.000 0.000 A
> 0.01317904 3.4363044e-05 CH2R 6 0.000 0.000 A 0.0073342096
> 2.8058209e-05 CR1 6 0.000 0.000 A 0.0055130625 1.5116544e-05
> HC 1 0.000 0.000 A 8.464e-05 1.5129e-08 H 1 0.000
> 0.000 A 0 0 DUM 0 0.000 0.000 A
> 0 0 S 16 0.000 0.000 A 0.0099840064 1.3075456e-05
> CU1+ 29 0.000 0.000 A 0.0004182025 5.1251281e-09 CU2+ 29
> 0.000 0.000 A 0.0004182025 5.1251281e-09 FE 26 0.000
> 0.000 A 0 0 ZN2+ 30 0.000 0.000 A
> 0.0004182025 9.4400656e-09 MG2+ 12 0.000 0.000 A 6.52864e-05
> 3.4082244e-09 CA2+ 20 0.000 0.000 A 0.00100489 4.9801249e-07 P
> 15 0.000 0.000 A 0.01473796 2.2193521e-05 AR 18 0.000
> 0.000 A 0.0062647225 9.847044e-06 F 9 0.000 0.000 A
> 0.0011778624 7.6073284e-07 CL 17 0.000 0.000 A 0.0087647044
> 1.5295921e-05 BR 35 0.000 0.000 A 0.02765569 6.5480464e-05
> CMet 6 0.000 0.000 A 0.0088755241 1.936e-05 OMet 8 0.000
> 0.000 A 0.0022619536 2.325625e-06 NA+ 11 0.000 0.000 A
> 7.2063121e-05 2.1025e-08 CL- 17 0.000 0.000 A 0.01380625
> 0.0001069156 CChl 6 0.000 0.000 A 0.0026308693 4.064256e-06
> CLChl 17 0.000 0.000 A 0.0083066819 1.3764842e-05 HChl 1
> 0.000 0.000 A 3.76996e-05 4.2999495e-09 SDmso 16 0.000
> 0.000 A 0.010561673 2.149806e-05 CDmso 6 0.000 0.000 A
> 0.0096138025 2.6646244e-05 ODmso 8 0.000 0.000 A 0.0022707131
> 7.5144626e-07 CCl4 6 0.000 0.000 A 0.0026308693 7.5999462e-06
> CLCl4 17 0.000 0.000 A 0.0076040144 1.2767758e-05 FTFE 9
> 0.000 0.000 A 0.0011778624 1e-06 CTFE 6 0.000 0.000
> A 0.0023406244 3.374569e-06 CHTFE 6 0.000 0.000 A
> 0.0071048041 2.5775929e-05 OTFE 8 0.000 0.000 A 0.0022619536
> 1.505529e-06 CUrea 6 0.000 0.000 A 0.0048868488 1.3589545e-05
> OUrea 8 0.000 0.000 A 0.0023639044 1.5898688e-06 NUrea 7
> 0.000 0.000 A 0.0033527574 3.9509513e-06 SI 14 0.000
> 0.000 A 0.01473796 2.2193521e-05 MNH3 0 0.000 0.000 A 0.0
> 0.0 MW 0 0.000 0.000 A 0.0 0.0
>
> And my topology---
>
> ; ; It was generated using program: ; pdb2gmx_d - VERSION 4.5.1 ; ; Command
> line was: ; /home/ubelix/l_insel_ria/l_watkins/bin/pdb2gmx_d -f
> /home/ubelix/l_insel_ria/l_watkins/gormacswork/With-without/TCR-MHC/Withpeptide/4thMD/TCRrev_MHC-pep.pdb
> -o
> /home/ubelix/l_insel_ria/l_watkins/gormacswork/With-without/TCR-MHC/Withpeptide/4thMD/TMPr1.pdb
> -ignh ; ; Force field was read from the standard Gromacs share directory. ;
>
> [ moleculetype ] ; Name nrexcl Protein_chain_A 3
>
> [ atoms ] ; nr type resnr residue atom cgnr charge mass
> typeB chargeB massB ; residue 1 PRO rtp PRO q +1.0 1 NT
> 1 PRO N 1 0.128 14.0067 ; qtot 0.128 2 H
> 1 PRO H1 1 0.248 1.008 ; qtot 0.376 3 H
> 1 PRO H2 1 0.248 1.008 ; qtot 0.624 4 CH1
> 1 PRO CA 2 0.188 13.019 ; qtot 0.812 5 CH2r
> 1 PRO CB 2 0 14.027 ; qtot 0.812 6 CR2r
> 1 PRO CG 3 0 14.027 ; qtot 0.812 7 CR2r
> 1 PRO CD 3 0.188 14.027 ; qtot 1 8 C 1
> PRO C 4 0.45 12.011 ; qtot 1.45 9 O 1
> PRO O 4 -0.45 15.9994 ; qtot 1 ; residue 2 GLN rtp GLN
> q 0.0....................
>
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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