[gmx-users] dialanine using charmm27 ff

[Sandeep Somani]

Hi

I am trying to set up a simulation for dialanine using charmm27 ff but am
getting errors in pdb2gmx due to missing definitions in rtp file.

I created the pdb file (below) using Charmm for the sequence
ACE-ALA-ALA-CT3.

pdb2gmx recognizes ALA atoms but not those of the terminal groups ACE and
CT3.

Does someone have the appropriate definitions for these residues ?
( I have tried http://swissparam.ch/ to generate an itp file for the
molecule, but upon using it in GMX it does not give the same energy as that
from charmm. )

I am using GMX4.5.4.

Thanks
Sandeep

--
Post Doc
Wales Research Group
Department of Chemistry
Cambridge

=============================================================
REMARK Charmm commands:
REMARK ! CONSTRUCT STRUCTURE FROM SEQUENCE
REMARK READ SEQUence CARD
REMARK *
REMARK 1
REMARK ALA ALA
REMARK GENErate DIALA FIRSt ACE LAST CT3 WARN SETUp
REMARK
ATOM      1  CAY ALA     1      -2.160   0.537   0.930  1.00  0.00      DIAL
ATOM      2  HY1 ALA     1      -2.466   0.003   0.005  1.00  0.00      DIAL
ATOM      3  HY2 ALA     1      -2.562   1.572   0.910  1.00  0.00      DIAL
ATOM      4  HY3 ALA     1      -2.562   0.001   1.816  1.00  0.00      DIAL
ATOM      5  CY  ALA     1      -0.672   0.582   1.009  1.00  0.00      DIAL
ATOM      6  OY  ALA     1      -0.105   1.128   1.954  1.00  0.00      DIAL
ATOM      7  N   ALA     1       0.000   0.000   0.000  1.00  0.00      DIAL
ATOM      8  HN  ALA     1      -0.453  -0.444  -0.769  1.00  0.00      DIAL
ATOM      9  CA  ALA     1       1.459   0.000   0.000  1.00  0.00      DIAL
ATOM     10  HA  ALA     1       1.812  -0.497   0.897  1.00  0.00      DIAL
ATOM     11  CB  ALA     1       1.949  -0.834  -1.207  1.00  0.00      DIAL
ATOM     12  HB1 ALA     1       1.514  -1.854  -1.155  1.00  0.00      DIAL
ATOM     13  HB2 ALA     1       1.628  -0.373  -2.167  1.00  0.00      DIAL
ATOM     14  HB3 ALA     1       3.056  -0.932  -1.214  1.00  0.00      DIAL
ATOM     15  C   ALA     1       2.096   1.401   0.000  1.00  0.00      DIAL
ATOM     16  O   ALA     1       1.425   2.432   0.000  1.00  0.00      DIAL
ATOM     17  N   ALA     2       3.451   1.458   0.000  1.00  0.00      DIAL
ATOM     18  HN  ALA     2       3.954   0.594   0.000  1.00  0.00      DIAL
ATOM     19  CA  ALA     2       4.276   2.664   0.000  1.00  0.00      DIAL
ATOM     20  HA  ALA     2       4.065   3.236  -0.897  1.00  0.00      DIAL
ATOM     21  CB  ALA     2       3.864   3.539   1.207  1.00  0.00      DIAL
ATOM     22  HB1 ALA     2       2.776   3.756   1.155  1.00  0.00      DIAL
ATOM     23  HB2 ALA     2       4.063   3.014   2.167  1.00  0.00      DIAL
ATOM     24  HB3 ALA     2       4.407   4.508   1.214  1.00  0.00      DIAL
ATOM     25  C   ALA     2       5.791   2.399   0.000  1.00  0.00      DIAL
ATOM     26  O   ALA     2       6.597   3.328   0.000  1.00  0.00      DIAL
ATOM     27  NT  ALA     2       6.175   1.110   0.000  1.00  0.00      DIAL
ATOM     28  HNT ALA     2       5.528   0.351   0.000  1.00  0.00      DIAL
ATOM     29  CAT ALA     2       7.566   0.777   0.000  1.00  0.00      DIAL
ATOM     30  HT1 ALA     2       8.048   1.201   0.907  1.00  0.00      DIAL
ATOM     31  HT2 ALA     2       7.683  -0.327   0.000  1.00  0.00      DIAL
ATOM     32  HT3 ALA     2       8.048   1.201  -0.907  1.00  0.00      DIAL
TER      33      ALA      2
END
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