[gmx-users] Error in free energy calculation
Tasneem Kausar
tasneemkausar12 at gmail.com
Fri Mar 17 06:32:56 CET 2017
Thank you everyone for your reply.
I have resolved the problem for reply of Justin from previous mail at gmx
list.
Thank you Justin again
On Thu, Mar 16, 2017 at 5:57 PM, Amir Zeb <zebamir85 at gmail.com> wrote:
> You probably follow umbrella sampling for free energy calculation.
> If it is so, you may change the position of your drug.itp file in topology
> file, means that before the protein topology.
> I hope this might solve your problem.
>
> Good luck!
>
> Amir
>
> On Thu, Mar 16, 2017 at 2:49 AM, Tasneem Kausar <tasneemkausar12 at gmail.com
> >
> wrote:
>
> > Dear All
> >
> > I am trying to perform free energy calculations of a protein drug system.
> > I am using Gromacs-5.1.4 for this purpose. decoulpe molecule type i.e.
> drug
> > molecule is defined in separate drug.itp file. From the discussions of
> > mailing list I have found that this is not a problem. To obtain the
> > equilibrium values for protein-ligand restraint 15 ns simulation was
> > performed. Here is the last section of topology file.
> > ; Include Position restraint file
> > #ifdef POSRES
> > #include "posre.itp"
> > #endif
> > #include "drug.itp"
> > [ intermolecular_interactions ]
> > [ bonds ]
> > ; i j type r0A r1A r2A fcA r0B r1B r2B
> > fcB
> > 1444 3118 10 0.591 0.591 10.0 0.0 0.591 0.591 10.0
> > 4184.000
> >
> > [ angle_restraints ]
> > ; ai aj ak al type thA fcA multA thB fcB
> > multB
> > 1431 1444 3118 1444 1 52.35 0.0 1 52.35 41.840
> 1
> > 1444 3118 3120 3118 1 118.14 0.0 1 118.14 41.840
> 1
> >
> > [ dihedral_restraints ]
> > ; ai aj ak al type phiA dphiA fcA phiB dphiB
> > fcB
> > 1444 1431 1444 3118 1 -99.41 0.0 0.0 -99.41 0.0
> > 41.840
> > 1431 1444 3118 3120 1 17.49 0.0 0.0 17.49 0.0
> > 41.840
> > 1444 3118 3120 3119 1 -6.49 0.0 0.0 -6.49 0.0
> > 41.840
> > ; Include water topology
> > #include "gromos54a7.ff/spc.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 "gromos54a7.ff/ions.itp"
> >
> > [ system ]
> > ; Name
> > DUMM in water t= 10000.00000
> > [ molecules ]
> > ; Compound #mols
> > Protein_chain_A 1
> > DRG 1
> > SOL 17685
> >
> > Is there any default position for [ intermolecular_interaction ] in
> > topology file.
> > Since I am using a drug.itp file for drug molecule. Numbering in itp file
> > starts from 1. Is atom number in itp file needed to be modified?
> >
> >
> > grompp gives many warning and 1 error
> > Back Off! I just backed up mdout.mdp to ./#mdout.mdp.9#
> >
> > WARNING 1 [file em_steep_0.mdp, line 78]:
> > Unknown left-hand 'pull_geometry' in parameter file
> >
> >
> >
> > WARNING 2 [file em_steep_0.mdp, line 78]:
> > Unknown left-hand 'pull_dim' in parameter file
> >
> >
> >
> > WARNING 3 [file em_steep_0.mdp, line 78]:
> > Unknown left-hand 'pull_start' in parameter file
> >
> >
> >
> > WARNING 4 [file em_steep_0.mdp, line 78]:
> > Unknown left-hand 'pull_init1' in parameter file
> >
> >
> >
> > WARNING 5 [file em_steep_0.mdp, line 78]:
> > Unknown left-hand 'pull_ngroups' in parameter file
> >
> >
> >
> > WARNING 6 [file em_steep_0.mdp, line 78]:
> > Unknown left-hand 'pull_group0' in parameter file
> >
> >
> >
> > WARNING 7 [file em_steep_0.mdp, line 78]:
> > Unknown left-hand 'pull_group1' in parameter file
> >
> >
> >
> > WARNING 8 [file em_steep_0.mdp, line 78]:
> > Unknown left-hand 'pull_k1' in parameter file
> >
> >
> >
> > WARNING 9 [file em_steep_0.mdp, line 78]:
> > Unknown left-hand 'pull_kB1' in parameter file
> >
> >
> >
> > NOTE 1 [file em_steep_0.mdp]:
> > With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
> > that with the Verlet scheme, nstlist has no effect on the accuracy of
> > your simulation.
> >
> > Setting the LD random seed to 1259182625
> > Generated 226 of the 1711 non-bonded parameter combinations
> >
> > -------------------------------------------------------
> > Program gmx grompp, VERSION 5.1.4
> > Source code file:
> > /home/shahid/Software/gromacs-5.1.4/src/gromacs/gmxpreprocess/topio.c,
> > line: 755
> >
> > Fatal error:
> > Syntax error - File complex.top, line 19956
> > Last line read:
> > '[ intermolecular_interactions ]'
> > Invalid order for directive intermolecular_interactions
> > For more information and tips for troubleshooting, please check the
> GROMACS
> > website at http://www.gromacs.org/Documentation/Errors
> > -------------------------------------------------------
> >
> > Here are mdp parameters
> >
> > ; Options for the decoupling
> > sc-alpha = 0.5
> > sc-coul = no
> > sc-power = 1
> > sc-sigma = 0.3
> > couple-moltype = DRG
> > couple-lambda0 = none
> > couple-lambda1 = vdw-q
> > couple-intramol = no
> > nstdhdl = 10
> > ; No velocities during EM
> > gen_vel = no
> > ; options for bonds
> > constraints = all_bonds
> > constraint-algorithm = lincs
> > continuation = no
> > lincs-order = 12
> > pull = no
> > pull_geometry = distance
> > pull_dim = N N Y
> > pull_start = yes
> > pull_init1 = 0.654
> > pull_ngroups = 1
> > pull_group0 = a_1444
> > pull_group1 = a_3118
> > pull_k1 = 0.0 ; kJ*mol^(-1)*nm^(-2)
> > pull_kB1 = 4184 ; kJ*mol^(-1)*nm^(-2)
> >
> > since I have defined restraint parameters for protein and drug. then what
> > is need of pulling code and why?
> >
> > Kindly resolve the issue.
> > Thanks in Advance.
> > Regards
> > --
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