[gmx-users] Re: gmx-users Digest, Vol 77, Issue 150
lloyd riggs
lloyd.riggs at gmx.ch
Fri Sep 24 11:30:04 CEST 2010
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 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....
>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....................
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