[gmx-users] coenzyme-protein complex
Justin Lemkul
jalemkul at vt.edu
Wed Jan 8 03:21:53 CET 2014
On 1/7/14, 1:45 PM, Mostafa Javaheri wrote:
> Dear J. Lemkul
> >> 3. I merged these two ligands into one mol2 file and
> >> sent it to the swissparam, then followed the rest of steps, is this OK or
> >> should I send them separately?
>
> >They should probably be treated individually.
>
> I treated these two ligands individually and faced the following error when run
> this command
>
> grompp -f em.mdp -c solvated.pdb -p topol.top
>
> ***********************
> Program grompp, VERSION 4.6.4
> Source code file: /home/MJ-centos/programfiles/gromacs-4.6.4/src/kernel/topio.c,
> line: 734
>
> Fatal error:
> Syntax error - File GTP.itp, line 7
> Last line read:
> '[ atomtypes ] '
> Invalid order for directive atomtypes
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> ************************
>
The [atomtypes] directive is at the force field level, so any new [atomtypes]
need to be declared before any [moleculetypes] appear in the topology. See
Chapter 5 for the required hierarchy.
> I added ligands to the end of conf.pdb file and modified topol.top too (these
> files uploaded for more details), but when I treat each of them separately no
> error will appear and I'll face just the following notes, am I doing something
> wrong?
>
> *************************
> Ignoring obsolete mdp entry 'title'
>
> NOTE 1 [file em.mdp]:
> The switch/shift interaction settings are just for compatibility; you
> will get better performance from applying potential modifiers to your
> interactions!
>
>
>
> NOTE 2 [file em.mdp]:
> For energy conservation with switch/shift potentials, rlist should be 0.1
> to 0.3 nm larger than rvdw.
>
These notes indicate possible problems with the .mdp file, but since you haven't
provided that file, it's impossible to say what may or may not be wrong. Notes
don't necessarily indicate real problems, but they often catch things that could
be bad.
-Justin
> Generated 24310 of the 24310 non-bonded parameter combinations
> Generating 1-4 interactions: fudge = 1
> Generated 21172 of the 24310 1-4 parameter combinations
> Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
> Excluding 3 bonded neighbours molecule type 'Other_chain_A2'
> Excluding 3 bonded neighbours molecule type 'GDP'
> Excluding 2 bonded neighbours molecule type 'SOL'
>
> NOTE 3 [file topol.top, line 48]:
> System has non-zero total charge: -43.999989
> Total charge should normally be an integer. See
> http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
> for discussion on how close it should be to an integer.
>
>
>
> Analysing residue names:
> There are: 899 Protein residues
> There are: 3 Other residues
> There are: 48875 Water residues
> Analysing Protein...
> Analysing residues not classified as Protein/DNA/RNA/Water and splitting into
> groups...
> Number of degrees of freedom in T-Coupling group rest is 334845.00
> Largest charge group radii for Van der Waals: 0.039, 0.039 nm
> Largest charge group radii for Coulomb: 0.084, 0.084 nm
>
> NOTE 4 [file em.mdp]:
> The sum of the two largest charge group radii (0.078024) is larger than
> rlist (1.200000) - rvdw (1.200000).
> With exact cut-offs, better performance can be obtained with
> cutoff-scheme = Verlet, because it does not use charge groups at all.
>
> Calculating fourier grid dimensions for X Y Z
> Using a fourier grid of 108x108x108, spacing 0.118 0.118 0.118
> Estimate for the relative computational load of the PME mesh part: 0.17
> This run will generate roughly 12 Mb of data
>
> There were 4 notes
> ****************************
>
> *************************
> ; Include forcefield parameters
> #include "charmm27.ff/forcefield.itp"
>
> ; Include chain topologies
> #include "GDP.itp"
> #include "GTP.itp"
> #include "topol_Protein_chain_A.itp"
> #include "topol_Other_chain_A2.itp"
>
> ; Include water topology
> #include "charmm27.ff/tip3p.itp"
>
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ; i funct fcx fcy fcz
> 1 1 1000 1000 1000
> #endif
>
> ; Include topology for ions
> #include "charmm27.ff/ions.itp"
>
> [ system ]
> ; Name
> A1CBIII in water
>
> [ molecules ]
> ; Compound #mols
> Protein_chain_A 1
> Other_chain_A2 2
> GDP 1
> GTP 1
> **************************
> topol.top
>
> **************************
> ATOM 13821 HZ3 LYS A 450 30.059 9.034 11.305 1.00 0.00
> ATOM 13822 C LYS A 450 25.373 4.382 14.445 1.00 0.00 C
> ATOM 13823 OT1 LYS A 450 24.583 4.846 13.578 1.00 0.00 O
> ATOM 13824 OT2 LYS A 450 25.029 4.012 15.600 1.00 0.00 O
> ATOM 13825 MG MG A 502 18.842 20.898 -18.829 1.00 0.00
> ATOM 13826 MG MG A 503 22.122 -11.947 -46.475 1.00 0.00
> ATOM 1 N1 LIG 1 15.320 -7.826 -42.055 1.00 0.00 LIG
> ATOM 2 C2 LIG 1 15.559 -8.569 -40.969 1.00 0.00 LIG
> ATOM 3 N3 LIG 1 16.562 -9.453 -40.896 1.00 0.00 LIG
> ATOM 4 C4 LIG 1 17.388 -9.635 -41.933 1.00 0.00 LIG
> ATOM 5 C5 LIG 1 17.190 -8.858 -43.145 1.00 0.00 LIG
> ATOM 6 C6 LIG 1 16.071 -7.910 -43.148 1.00 0.00 LIG
> ATOM 7 N7 LIG 1 18.142 -9.240 -43.995 1.00 0.00 LIG
> ATOM 8 C8 LIG 1 18.889 -10.176 -43.380 1.00 0.00 LIG
> ATOM 9 N9 LIG 1 18.422 -10.414 -42.154 1.00 0.00 LIG
> ATOM 10 PA LIG 1 23.028 -10.344 -43.330 1.00 0.00 LIG
> ATOM 11 PB LIG 1 25.620 -9.375 -44.053 1.00 0.00 LIG
> ATOM 12 HN1 LIG 1 14.522 -7.160 -42.047 1.00 0.00 LIG
> ATOM 13 HN21 LIG 1 13.999 -7.791 -39.898 1.00 0.00 LIG
> ATOM 14 HN22 LIG 1 14.946 -9.000 -39.071 1.00 0.00 LIG
> ATOM 15 HO2' LIG 1 17.694 -14.312 -41.107 1.00 0.00 LIG
> ATOM 16 HO3' LIG 1 19.145 -14.258 -39.324 1.00 0.00 LIG
> ATOM 17 H1' LIG 1 18.474 -11.141 -40.186 1.00 0.00 LIG
> ATOM 18 C1' LIG 1 18.971 -11.324 -41.145 1.00 0.00 LIG
> ATOM 19 O1A LIG 1 22.215 -10.966 -44.397 1.00 0.00 LIG
> ATOM 20 O1B LIG 1 25.597 -8.334 -42.987 1.00 0.00 LIG
> ATOM 21 N2 LIG 1 14.767 -8.443 -39.892 1.00 0.00 LIG
> ATOM 22 H2' LIG 1 18.953 -12.957 -42.525 1.00 0.00 LIG
> ATOM 23 O2' LIG 1 17.693 -13.365 -40.927 1.00 0.00 LIG
> ATOM 24 C2' LIG 1 18.876 -12.794 -41.444 1.00 0.00 LIG
> ATOM 25 O2A LIG 1 22.715 -8.939 -42.977 1.00 0.00 LIG
> ATOM 26 O2B LIG 1 25.137 -8.949 -45.378 1.00 0.00 LIG
> ATOM 27 H3' LIG 1 20.489 -14.209 -41.283 1.00 0.00 LIG
> ATOM 28 O3' LIG 1 19.851 -13.606 -39.393 1.00 0.00 LIG
> ATOM 29 C3' LIG 1 20.108 -13.325 -40.758 1.00 0.00 LIG
> ATOM 30 O3A LIG 1 24.600 -10.498 -43.567 1.00 0.00 LIG
> ATOM 31 O3B LIG 1 26.905 -10.109 -44.110 1.00 0.00 LIG
> ATOM 32 C4' LIG 1 21.106 -12.199 -40.850 1.00 0.00 LIG
> ATOM 33 H4' LIG 1 21.694 -12.150 -39.926 1.00 0.00 LIG
> ATOM 34 O4' LIG 1 20.352 -11.019 -41.028 1.00 0.00 LIG
> ATOM 35 O5' LIG 1 22.921 -11.276 -42.060 1.00 0.00 LIG
> ATOM 36 C5' LIG 1 22.032 -12.368 -42.035 1.00 0.00 LIG
> ATOM 37 O6 LIG 1 15.833 -7.213 -44.138 1.00 0.00 LIG
> ATOM 38 H8 LIG 1 19.743 -10.671 -43.820 1.00 0.00 LIG
> ATOM 39 HC1 LIG 1 21.451 -12.391 -42.957 1.00 0.00 LIG
> ATOM 40 HC2 LIG 1 22.594 -13.296 -41.932 1.00 0.00 LIG
> ATOM 1 N1 LIG 1 9.682 24.014 -12.907 1.00 0.00 LIG
> ATOM 2 C2 LIG 1 9.758 23.159 -11.827 1.00 0.00 LIG
> ATOM 3 N3 LIG 1 10.590 22.064 -11.861 1.00 0.00 LIG
> ATOM 4 C4 LIG 1 11.311 21.834 -13.005 1.00 0.00 LIG
> ATOM 5 C5 LIG 1 11.227 22.665 -14.115 1.00 0.00 LIG
> ATOM 6 C6 LIG 1 10.400 23.782 -14.066 1.00 0.00 LIG
> ATOM 7 N7 LIG 1 12.055 22.162 -15.063 1.00 0.00 LIG
> ATOM 8 C8 LIG 1 12.646 21.043 -14.578 1.00 0.00 LIG
> ATOM 9 N9 LIG 1 12.164 20.814 -13.313 1.00 0.00 LIG
> ATOM 10 PA LIG 1 16.489 20.307 -14.720 1.00 0.00 LIG
> ATOM 11 PB LIG 1 19.173 20.886 -15.662 1.00 0.00 LIG
> ATOM 12 PG LIG 1 20.804 18.982 -17.141 1.00 0.00 LIG
> ATOM 13 HN1 LIG 1 9.071 24.853 -12.849 1.00 0.00 LIG
> ATOM 14 HN21 LIG 1 9.133 22.823 -9.905 1.00 0.00 LIG
> ATOM 15 HN22 LIG 1 8.433 24.232 -10.690 1.00 0.00 LIG
> ATOM 16 HO2' LIG 1 10.561 18.744 -11.934 1.00 0.00 LIG
> ATOM 17 HO3' LIG 1 12.256 17.706 -10.567 1.00 0.00 LIG
> ATOM 18 H1' LIG 1 12.161 19.933 -11.405 1.00 0.00 LIG
> ATOM 19 C1' LIG 1 12.580 19.766 -12.397 1.00 0.00 LIG
> ATOM 20 O1A LIG 1 15.523 20.116 -15.857 1.00 0.00 LIG
> ATOM 21 O1B LIG 1 18.861 21.695 -16.855 1.00 0.00 LIG
> ATOM 22 O1G LIG 1 19.697 19.159 -18.131 1.00 0.00 LIG
> ATOM 23 N2 LIG 1 9.052 23.428 -10.716 1.00 0.00 LIG
> ATOM 24 O2' LIG 1 10.956 18.001 -12.436 1.00 0.00 LIG
> ATOM 25 H2' LIG 1 12.337 18.289 -13.945 1.00 0.00 LIG
> ATOM 26 C2' LIG 1 12.244 18.357 -12.861 1.00 0.00 LIG
> ATOM 27 O2A LIG 1 16.484 21.702 -14.124 1.00 0.00 LIG
> ATOM 28 O2B LIG 1 19.525 21.804 -14.510 1.00 0.00 LIG
> ATOM 29 O2G LIG 1 22.061 19.629 -17.641 1.00 0.00 LIG
> ATOM 30 C3' LIG 1 13.345 17.554 -12.193 1.00 0.00 LIG
> ATOM 31 O3' LIG 1 13.110 17.303 -10.830 1.00 0.00 LIG
> ATOM 32 H3' LIG 1 13.537 16.635 -12.746 1.00 0.00 LIG
> ATOM 33 O3A LIG 1 17.934 19.926 -15.322 1.00 0.00 LIG
> ATOM 34 O3B LIG 1 20.367 19.829 -15.797 1.00 0.00 LIG
> ATOM 35 O3G LIG 1 21.062 17.602 -16.613 1.00 0.00 LIG
> ATOM 36 C4' LIG 1 14.535 18.498 -12.308 1.00 0.00 LIG
> ATOM 37 H4' LIG 1 15.199 18.371 -11.453 1.00 0.00 LIG
> ATOM 38 O4' LIG 1 14.003 19.820 -12.356 1.00 0.00 LIG
> ATOM 39 O5' LIG 1 16.345 19.168 -13.634 1.00 0.00 LIG
> ATOM 40 C5' LIG 1 15.290 18.246 -13.603 1.00 0.00 LIG
> ATOM 41 O6 LIG 1 10.297 24.576 -15.019 1.00 0.00 LIG
> ATOM 42 H8 LIG 1 13.378 20.430 -15.103 1.00 0.00 LIG
> ATOM 43 HC1 LIG 1 15.679 17.228 -13.620 1.00 0.00 LIG
> ATOM 44 HC2 LIG 1 14.630 18.407 -14.456 1.00 0.00 LIG
> TER
> ENDMDL
> ***************************
> conf.pdb
>
>
> On Mon, 01/06/2014 05:30 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
> On 1/6/14, 5:35 AM, Mostafa Javaheri wrote:
> > Dear Gromacs users
> > I would be grateful if any one answers my questions
> > 1.
> > I have two coenzyme (GTP & GDP) and two Ion (Mg) attached to the
> > hetrodimer protein, I am going to use charmm27 force field for Gromacs
> simulation and swissparam for achieving the ligands topologies; Could I
> trust at these topology (.itp) or they need
> > some charge correction like PRODRG outputs?
>
> That depends on the quality of the output charges. SwissParam, to my knowledge,
> does not score the quality of the topology itself, though validation was done
> based on reproducing binding energies in the original paper. That does not (in
> my opinion) necessarily guarantee that any topology it produces will be of high
> quality.
>
> The ParamChem server provides a more quantitative score of the quality of the
> topology. The larger the penalty score, the more refinement you need to do.
> The procedure for improving the topology is published and is also written as a
> web tutorial. The other benefit of ParamChem is that it has recently been
> updated to the latest version of the CGenFF parameter set (2b8) and is thus
> up-to-date with the latest CHARMM force fields (with CHARMM36 representing
> improvements over CHARMM27).
>
> > 2. Does anyone have ".mdp" fiels that consist with my system?
>
> CHARMM parameters have been discussed extensively across the list. The settings
> are dependent upon the force field, not the contents of the coordinate file.
>
> > 3. I merged these two ligands into one mol2 file and
> > sent it to the swissparam, then followed the rest of steps, is this OK or
> > should I send them separately?
>
> They should probably be treated individually.
>
> -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 <mailto:jalemkul at outerbanks.umaryland.edu>
> | (410) 706-7441
>
> ==================================================
> --
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--
==================================================
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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