[gmx-users] Simulating an alkanethiol SAM on gold: atom type not recognized when running pdb2gmx

[Olivia Waring]

Hello GROMACS users,

I wish to simulate an alkanethiol self-assembled monolayer on a gold
surface. The first molecule I am attempting to model is quite simple:
CH3(CH2)11S. I have constructed a united atom force field based on
parameters published by Hautman and Klein (J. Chem. Phys. 1989) to represent
the alkanethiol chain. I wrote an rtp file containing a single residue [ ALK
] which contains the following list of atoms:

[ ALK ]
 [ atoms ]
 ; name type charge   chargegroup
   CH3  CH3   0.000   1
   CH2A CH2   0.000   1
   CH2B CH2   0.000   1
   CH2C CH2   0.000   1
   CH2D CH2   0.000   1
   CH2E CH2   0.000   1
   CH2F CH2   0.000   1
   CH2G CH2   0.000   1
   CH2H CH2   0.000   1
   CH2I CH2   0.000   1
   CH2J CH2   0.000   1
   CH2K CH2   0.000   1
   S    S    0.000   1

I have defined the CH3, CH2, and S atom types in an atomtypes.atp file. I
used PRODRG to generate an all-atom pdb file representing my alkanethiol,
which I then manually modified to reflect my united atom approach. Here is
an excerpt:

HETATM    1  CH3        ALK     1      -0.920  -1.820  -0.970  1.00 20.00
          C
HETATM    2  CH2A       ALK     1      -0.010  -2.270   0.170  1.00 20.00
          C
HETATM    3  CH2B       ALK     1       0.240  -3.780   0.060  1.00 20.00
          C
HETATM    4  CH2C       ALK     1       1.140  -4.290   1.190  1.00 20.00
          C
HETATM    5  CH2D       ALK     1       0.420  -4.310   2.540  1.00 20.00
          C
HETATM    6  CH2E       ALK     1       1.310  -4.850   3.660  1.00 20.00
          C
HETATM    7  CH2F       ALK     1       1.530  -6.360   3.540  1.00 20.00
          C
HETATM    8  CH2G       ALK     1       2.420  -6.850   4.680  1.00 20.00
          C
HETATM    9  CH2H       ALK     1       2.630  -8.360   4.540  1.00 20.00
          C
HETATM   10  CH2I       ALK     1       3.510  -8.860   5.700  1.00 20.00
          C
HETATM   11  CH2J       ALK     1       3.750 -10.370   5.610  1.00 20.00
          C
HETATM   12  CH2K       ALK     1       2.490 -11.170   5.960  1.00 20.00
          C
HETATM   12  S          ALK     1       2.730 -12.980   5.840  1.00 20.00
          S

When I try to run pdb2gmx on my coordinate file, I get the following error:

Atom CH2 in residue ALK 0 was not found in rtp entry ALK with 13 atoms while
sorting atoms.

Although I have read through a significant portion of the manual, I am a
very new GROMACS user, and have most likely made numerous mistakes!! If
someone could please point out how to address this error and anything else I
might be missing, I would appreciate it very much. Any general tips for
constructing a system from scratch are also quite welcome.

Thank you in advance,
O. M. W.



-- 
Olivia Waring (王维娅)
Princeton University '12
AB Chemistry
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