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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