[gmx-users] NMR restrained MD
Justin Lemkul
jalemkul at vt.edu
Thu Sep 12 21:14:58 CEST 2013
On 9/12/13 2:57 PM, Rama Krishna Koppisetti wrote:
> Hi Justin,
> Output topology from pdb2gmx. You could see some entries differ between
> two molecules.
>
> I'm looking forward to do restrained MD for this system by using Gromacs.
>
> [ moleculetype ]
> ; Name nrexcl
> Protein 3
>
> [ atoms ]
> ; nr type resnr residue atom cgnr charge mass
> typeB chargeB massB
> ; residue 100 PHE rtp PHE q +1.0
> 1 opls_287 100 PHE N 1 -0.3 14.0067 ;
> qtot -0.3
> 2 opls_290 100 PHE H1 1 0.33 1.008 ;
> qtot 0.03
> 3 opls_290 100 PHE H2 1 0.33 1.008 ;
> qtot 0.36
> 4 opls_290 100 PHE H3 1 0.33 1.008 ;
> qtot 0.69
> 5 opls_293B 100 PHE CA 1 0.25 12.011 ;
> qtot 0.94
> 6 opls_140 100 PHE HA 1 0.06 1.008 ;
> qtot 1
> 7 opls_149 100 PHE CB 2 -0.005 12.011 ;
> qtot 0.995
>
> ; residue 1 DMPC rtp DMPC q 0.0
> 2514 LC3 1 DMPC CN1 874 0.4 15.035 ;
> qtot 8.4
> 2515 LC3 1 DMPC CN2 874 0.4 15.035 ;
> qtot 8.8
> 2516 LC3 1 DMPC CN3 874 0.4 15.035 ;
> qtot 9.2
> 2517 LNL 1 DMPC NTM 874 -0.5 14.0067 ;
> qtot 8.7
> 2518 LH2 1 DMPC CA 874 0.3 14.027 ;
> qtot 9
> 2519 LC2 1 DMPC CB 875 0.4 14.027 ;
> qtot 9.4
> 2520 LOS 1 DMPC OA 875 -0.8 15.9994 ;
> qtot 8.6
> 2521 LP 1 DMPC P 875 1.7 30.9738 ;
> qtot 10.3
> 2522 LOM 1 DMPC OB 875 -0.8 15.9994 ;
> qtot 9.5
> 2523 LOM 1 DMPC OC 875 -0.8 15.9994 ;
> qtot 8.7
> 2524 LOS 1 DMPC OD 875 -0.7 15.9994 ;
> qtot 8
> 2525 LC2 1 DMPC CC 876 0.4 14.027 ;
> qtot 8.4
> 2526 LH1 1 DMPC CD 876 0.3 13.019 ;
> qtot 8.7
> 2527 LOS 1 DMPC OE 876 -0.7 15.9994 ;
> qtot 8
>
> [ bonds ]
> ; ai aj funct c0 c1 c2 c3
> ;bonds for protein
> 1 2 1
> 1 3 1
> 1 4 1
> 1 5 1
> 5 6 1
> 5 7 1
> 5 21 1
> 7 8 1
> 7 9 1
> 7 10 1
> ;bonds from lipid atoms
> 2514 2517 1 0.1470 8.7100e+06
> 2515 2517 1 0.1470 8.7100e+06
> 2516 2517 1 0.1470 8.7100e+06
> 2517 2518 1 0.1470 8.7100e+06
> 2518 2519 1 0.1530 7.1500e+06
> 2519 2520 1 0.1430 8.1800e+06
> 2520 2521 1 0.1610 4.8400e+06
>
I don't see anything syntactically wrong here. The normal function of the
OPLS-AA force field is to look up all bonded parameters from ffbonded.itp (hence
why the lines above for the protein atoms appear to have no parameters
assigned). In principle, you can specify them explicitly, so I don't know why
grompp is complaining.
> [ pairs ]
> ; ai aj funct c0 c1 c2 c3
> 1 8 1
> 1 9 1
> 1 10 1
> 1 22 1
> 1 23 1
> 2 6 1
> 2 7 1
> 2 21 1
> 3 6 1
> 3 7 1
> 3 21 1
> 4 6 1
> 4 7 1
> 4 21 1
> 5 11 1
> 5 13 1
> [ angles ]
> ; ai aj ak funct c0 c1
> c2 c3
> ;angles for protein atoms
> 2 1 3 1
> 2 1 4 1
> 2 1 5 1
> 3 1 4 1
> 3 1 5 1
> 4 1 5 1
> 1 5 6 1
> 1 5 7 1
> 1 5 21 1
> 6 5 7 1
> 6 5 21 1
> ;angles for lipid atoms
> 2514 2517 2515 1 109.50 520.00
> 2514 2517 2516 1 109.50 520.00
> 2514 2517 2518 1 109.50 520.00
> 2515 2517 2516 1 109.50 520.00
> 2515 2517 2518 1 109.50 520.00
> 2516 2517 2518 1 109.50 520.00
> 2517 2518 2519 1 111.00 530.00
> 2518 2519 2520 1 111.00 530.00
> 2519 2520 2521 1 120.00 530.00
> 2520 2521 2522 1 109.60 450.00
> [ dihedrals ]
> ; ai aj ak al funct c0 c1
> c2 c3 c4 c5
> ;For protein
> 2 1 5 6 3
> 2 1 5 7 3
> 2 1 5 21 3
> 23 25 27 30 3 dih_ARG_chi1_N_C_C_C
> 45 25 27 30 3 dih_ARG_chi1_C_C_C_CO
> ;For lipids
> 2516 2517 2518 2519 3 1 0.00 3.77 3
> 2514 2517 2518 2519 3
> 2515 2517 2518 2519 3
> 2517 2518 2519 2520 3 1 0.00 8.62 3
> 2518 2519 2520 2521 3 1 0.00 3.77 3
> 2519 2520 2521 2524 3 1 0.00 3.19 3
> 2519 2520 2521 2522 3
> 2519 2520 2521 2523 3
> 2520 2521 2524 2525 3 1 0.00 3.19 3
>
Note here that the dihedral entries are garbage. The parameters you have are
periodic dihedrals, not R-B, but the topology is specifying the phase angle,
force constant, and multiplicity as coefficients in the R-B expression. You
have two options here that may work:
1. Manually fix the topology such that these dihedrals are actually represented
as periodic (i.e. delete the function type 3 that tells grompp they should be R-B)
2. Make an entirely separate lipid.rtp file (containing only the DMPC entry)
that uses periodic dihedrals. I don't know if this approach will work, to be
quite honest. Given that there need to be both R-B and periodic dihedrals in
these molecules, there is no real easy way out.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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