[gmx-users] coenzyme-protein complex
Mostafa Javaheri
m.javaheri at gu.ac.ir
Tue Jan 7 20:00:43 CET 2014
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
************************
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.
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 | (410) 706-7441
>
> ==================================================
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