Re: FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR CT2 CT1 CT2 (ATOMS 107 98 100)

From: johan strumpfer (johanstr_at_ks.uiuc.edu)
Date: Sun Oct 23 2011 - 16:42:07 CDT

Hi Jens,

You must have changed something:
In the charmm ILE topology there is:
ATOM CG2 CT3 -0.27

but in your topology there is:
ATOM CG2 CT2 -0.18

It looks to me light some renaming occurred...

Cheers,
Johan

------------------------------------------------------------------------------------------------------
Johan Strumpfer:         johanstr_at_ks.uiuc.edu        www.ks.uiuc.edu/~johanstr
Theoretical and Computational Biophysics Group
3115 Beckman Institute
University of Illinois at Urbana-Champaign
405 N. Mathews
Urbana, IL 61801, USA
------------------------------------------------------------------------------------------------------

On Sun, Oct 23, 2011 at 3:39 PM, Jens K. Munk <jkm_at_life.ku.dk> wrote:
> Dear NAMD-L,
>
> I know this topic has been dealt with previously here, but the previous solutions do not seem to apply to my system. I hope I am not overlooking something obvious.
>
> I am using unnatural amino acids and one of these is 2-amino-3-ethylpentanoic acid, or EPA for short. It is like ILE only the two chains branching out from the beta carbon are both ethyls whereas in ILE they are one ethyl and one methyl.
>
> To make a topology file I extended the methyl group to an ethyl groyp. I made sure to add the new bonds and rename kept atoms appropriately. In the topology file IC table I commented out anything that might contain erroneous information.
>
> I constructed a .pdb by manually "methylating" ILE in a .pdb I have from NMR. I made sure the atom names in the .pdb agreed with those in the topology file. I successfully created .psf.
>
> Now I want to minimize the system in vacuum since this manual editing has probably given rise to suboptimal bonds and angles.
>
> Then comes the mentioned error:
>
> FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR CT2 CT1 CT2 (ATOMS 107 98 100)
>
> These atoms are beta carbon (#98) and the two gamma carbons (#s 107 and 103). This surprises me since I have not done anything to these atoms.
>
> Please help!
>
> File snips:
>
> ---
>
> .psf:
>
>      94 E    6    EPA  N    NH1   -0.470000       14.0070           0
>      95 E    6    EPA  HN   H      0.310000        1.0080           0
>      96 E    6    EPA  CA   CT1    0.070000       12.0110           0
>      97 E    6    EPA  HA   HB     0.090000        1.0080           0
>      98 E    6    EPA  CB   CT1   -0.090000       12.0110           0
>      99 E    6    EPA  HB   HA     0.090000        1.0080           0
>     100 E    6    EPA  CG2  CT2   -0.180000       12.0110           0
>     101 E    6    EPA  HG21 HA     0.090000        1.0080           0
>     102 E    6    EPA  HG22 HA     0.090000        1.0080           0
>     103 E    6    EPA  CD2  CT3   -0.270000       12.0110           0
>     104 E    6    EPA  HD21 HA     0.090000        1.0080           0
>     105 E    6    EPA  HD22 HA     0.090000        1.0080           0
>     106 E    6    EPA  HD23 HA     0.090000        1.0080           0
>     107 E    6    EPA  CG1  CT2   -0.180000       12.0110           0
>     108 E    6    EPA  HG11 HA     0.090000        1.0080           0
>     109 E    6    EPA  HG12 HA     0.090000        1.0080           0
>     110 E    6    EPA  CD1  CT3   -0.270000       12.0110           0
>     111 E    6    EPA  HD11 HA     0.090000        1.0080           0
>     112 E    6    EPA  HD12 HA     0.090000        1.0080           0
>     113 E    6    EPA  HD13 HA     0.090000        1.0080           0
>     114 E    6    EPA  C    C      0.510000       12.0110           0
>     115 E    6    EPA  O    O     -0.510000       15.9990           0
>
> ---
>
> .pdb:
>
> ATOM     94  N   EPA A   6      10.312  -1.918   1.897  1.00  0.00      E    N
> ATOM     95  HN  EPA A   6       9.341  -1.756   2.060  1.00  0.00      E    H
> ATOM     96  CA  EPA A   6      11.200  -1.097   2.711  1.00  0.00      E    C
> ATOM     97  HA  EPA A   6      11.854  -0.554   2.045  1.00  0.00      E    H
> ATOM     98  CB  EPA A   6      10.410  -0.078   3.553  1.00  0.00      E    C
> ATOM     99  HB  EPA A   6       9.738  -0.622   4.199  1.00  0.00      E    H
> ATOM    100  CG2 EPA A   6       9.593   0.843   2.644  1.00  0.00      E    C
> ATOM    101 HG21 EPA A   6       8.928   0.261   2.176  1.00  0.00      E    H
> ATOM    102 HG22 EPA A   6      10.258   1.340   1.955  1.00  0.00      E    H
> ATOM    103  CD2 EPA A   6       8.825   1.908   3.396  1.00  0.00      E    C
> ATOM    104 HD21 EPA A   6       8.487   1.508   4.341  1.00  0.00      E    H
> ATOM    105 HD22 EPA A   6       9.466   2.758   3.572  1.00  0.00      E    H
> ATOM    106 HD23 EPA A   6       7.971   2.216   2.811  1.00  0.00      E    H
> ATOM    107  CG1 EPA A   6      11.355   0.733   4.427  1.00  0.00      E    C
> ATOM    108 HG11 EPA A   6      11.997   1.235   3.847  1.00  0.00      E    H
> ATOM    109 HG12 EPA A   6      11.901   0.068   5.079  1.00  0.00      E    H
> ATOM    110  CD1 EPA A   6      10.542   1.728   5.276  1.00  0.00      E    C
> ATOM    111 HD11 EPA A   6       9.564   1.302   5.496  1.00  0.00      E    H
> ATOM    112 HD12 EPA A   6      11.027   1.914   6.131  1.00  0.00      E    H
> ATOM    113 HD13 EPA A   6      10.429   2.585   4.773  1.00  0.00      E    H
> ATOM    114  C   EPA A   6      12.047  -1.960   3.640  1.00  0.00      E    C
> ATOM    115  O   EPA A   6      13.246  -1.728   3.799  1.00  0.00      E    O
>
> ---
> Topology:
>
> RESI EPA         0.00   !2-amino-3-ethylpentanoic acid, by jkm_at_life.ku.dk
> GROUP
> ATOM N    NH1    -0.47  !     |HG21 HG22 HD21 HD22
> ATOM HN   H       0.31  !  HN-N    \ /    |  /
> ATOM CA   CT1     0.07  !     |     CG2---CD2--HD23
> ATOM HA   HB      0.09  !     |    /
> GROUP                   !  HA-CA--CB-HB    HD11
> ATOM CB   CT1    -0.09  !     |    \       /
> ATOM HB   HA      0.09  !     |     CG1--CD1--HD12
> GROUP                   !   O=C    / \     \
> ATOM CG2  CT2    -0.18  !     | HG11 HG12  HD13
> ATOM HG21 HA      0.09
> ATOM HG22 HA      0.09
> !ATOM HG23 HA      0.09 ! HG23 removed to change from Ile to Epa, also CG2 charge
> GROUP                   ! changed from -0.27
> ATOM CD2  CT3    -0.27  ! Added
> ATOM HD21 HA      0.09  ! to
> ATOM HD22 HA      0.09  ! make
> ATOM HD23 HA      0.09  ! Epa
> GROUP
> ATOM CG1  CT2    -0.18
> ATOM HG11 HA      0.09
> ATOM HG12 HA      0.09
> GROUP
> ATOM CD1  CT3    -0.27
> ATOM HD11 HA      0.09
> ATOM HD12 HA      0.09
> ATOM HD13 HA      0.09
> GROUP
> ATOM C    C       0.51
> ATOM O    O      -0.51
> BOND CB  CA   CG1 CB   CG2 CB   CD1 CG1
> BOND N   HN   N   CA    C   CA   C   +N
> BOND CA  HA   CB  HB   CG1 HG11 CG1 HG12 CG2 HG21
> BOND CG2 HG22 CG2 CD2 CD1 HD11 CD1 HD12 CD1 HD13 !HG23 changed to CD2
> BOND CD2 HD21 CD2 HD22 CD2 HD23 !CH3 group added
> DOUBLE  O   C
> IMPR N -C CA HN  C CA +N O
> CMAP -C  N  CA  C   N  CA  C  +N
> DONOR HN N
> ACCEPTOR O C
> IC -C   CA   *N   HN    1.3470 124.1600  180.0000 114.1900  0.9978 !backbone
> IC -C   N    CA   C     1.3470 124.1600  180.0000 106.3500  1.5190 !backbone
> IC N    CA   C    +N    1.4542 106.3500  180.0000 117.9700  1.3465 !backbone
> IC +N   CA   *C   O     1.3465 117.9700  180.0000 120.5900  1.2300 !backbone
> IC CA   C    +N   +CA   1.5190 117.9700  180.0000 124.2100  1.4467 !backbone
>
> IC N    C    *CA  CB    1.4542 106.3500  124.2200 112.9300  1.5681 !CB rel bb
> IC N    C    *CA  HA    1.4542 106.3500 -115.6300 106.8100  1.0826 !HA rel bb
>
> IC N    CA   CB   CG1   1.4542 112.7900  180.0000 113.6300  1.5498 !CG1 away from N
> IC CG1  CA   *CB  HB    1.5498 113.6300  114.5500 104.4800  1.1195 !HB up
> IC CG1  CA   *CB  CG2   1.5498 113.6300 -130.0400 113.9300  1.5452 !CG2 down
>
> !IC CA   CB   CG2  HG21  1.5681 113.9300 -171.3000 110.6100  1.1100 !Removed to
> !IC HG21 CB   *CG2 HG22  1.1100 110.6100  119.3500 110.9000  1.1102 !change from
> !IC HG21 CB   *CG2 HG23  1.1100 110.6100 -120.0900 110.9700  1.1105 !Ile to Epa
>
> IC CA   CB   CG1  CD1   1.5681 113.6300  180.0000 114.0900  1.5381 !CD1 away from CA
> IC CD1  CB   *CG1 HG11  1.5381 114.0900  122.3600 109.7800  1.1130 !HG11 up
> IC CD1  CB   *CG1 HG12  1.5381 114.0900 -120.5900 108.8900  1.1141 !HG12 down
> IC CB   CG1  CD1  HD11  1.5498 114.0900 -176.7800 110.3100  1.1115 !\
> IC HD11 CG1  *CD1 HD12  1.1115 110.3100  119.7500 110.6500  1.1113 ! |CD1 Hs
> IC HD11 CG1  *CD1 HD13  1.1115 110.3100 -119.7000 111.0200  1.1103 !/
>
>
>
> --
> Venlig hilsen / Kind Regards
> M. Sc. Jens K. Munk
> Ph.D.-student
> Department of Basic Sciences and the Environment
> KU-LIFE
> Room T432
> Phone +45 3533 2429
> Thorvaldsensvej 40
> DK-1870 Frederiksberg
> Denmark
>
>
>
>

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