[gmx-users] Protein-ligand complex simulation and ATBserver file
Prasanth G, Research Scholar
prasanthghanta at sssihl.edu.in
Thu Dec 20 16:05:11 CET 2018
Dear Sir,
Thanks a lot for the inputs. I tried incorporating the forcefield
parameters (directory) obtained from the atbserver in the working
directory. When i was trying to convert the protein.pdb to .gro, I noticed
that the forcefield showed up in the menu as one included in local
directory, just as it does for cgenff in the tutorial.
I chose it to prepare the protein.gro file and then incorporated the
jz4.itp into the topology file of protein.
I was able to overcome the issues and complete npt and nvt equilibration.
Will proceed with the mdrun tomorrow morning.
Can you please suggest a solution for resuming the mdrun, in case there is
an interruption in the connectivity with the server. As i am running the
simulation from a laptop, I might not be able to leave it on through out.
Thank you once again.
---------------
Your #include statements are out of order. The #include statement for the
parent force field (the line above) should appear before anything else in
the topology, as it defines the atom types. The ffnonbonded.itp file does,
in fact, define CAro, which is a nonstandard type from ATB. I also suspect
that your specified PATH is lacking an initial / - note that full PATH
information is not necessary if the force field subdirectory is in $GMXLIB
or in the working directory.
-Justin
--
==========================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall
Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com
==========================================
On Wed, Dec 19, 2018 at 3:05 PM Prasanth G, Research Scholar <
prasanthghanta at sssihl.edu.in> wrote:
> Dear Sir,
>
> I am running GROMACS 5.1.4 on a server.
> I had converted the protein(pdb2gro) using the latest GROMOS forcefield.
> As per your suggestion, I had downloaded the parameter files from ATB
> server. As per the readme file from the server (in the parameters folder),
> i had updated my topol.top like this and also included the extracted folder
> to the working directory on the server.
> ---
> ; Include Position restraint file
> #ifdef POSRES
> #include "posre.itp"
> #endif
>
> ; Include ligand topology
> #include "jz4.itp"
>
> ; Include force field parameters
> #include "home/bio1/PG/gromos54a7_atb.ff/forcefield.itp"
>
> ; Include topology for ions
> #include "home/bio1/PG/gromos54a7_atb.ff/ions.itp"
>
> ; Include water topology
> #include "home/bio1/PG/gromos54a7_atb.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
>
> [ system ]
> ; Name
> LYSOZYME
>
> [ molecules ]
> ; Compound #mols
> Protein_chain_A 1
> JZ4 1
> ------------
> However, when i try to execute the grompp to add ions, the error still
> persists-
>
> *Fatal error:*
>
> *Atomtype CAro not found *
>
> Could you please tell me, if i have to change the way this has to be
> done. Here is the list of parameter files obtained from the ATBserver.
> link- https://atb.uq.edu.au/molecule.py?molid=342699#panel-md
> ---
> aminoacids.c.tdb, aminoacids.hbd, amonoacids.n.tbb, aminoacids.r2b,
> aminoacids.rtp, aminoacids.vsd, atomtypes.atp, dppc.itp, ffbonded.itp,
> ffdum.itp, ffnonbonded.itp, forcefield.doc, forcefield.itp, ions.itp,
> popc.itp, README.md, spc.itp, spce.itp, tip3.itp, tip4.itp, tmcl.itp,
> watermodels.dat
> ---
>
> Thanks in advance,
> Prasanth.
>
> ----------------------------------------------------------------------------
> Are you trying to combine this ligand topology with the CHARMM protein
> topology generated in the tutorial? If so, that's fundamentally incorrect
> and you can never make that work.
>
> If you're doing things entirely within the context of GROMOS, then you
> likely need additional files from the ATB server that provide parameters
> for the "unknown" atom types.
>
> -Justin
> --
>
> ==========================================
>
> Justin A. Lemkul, Ph.D.
>
> Assistant Professor
>
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
>
> ==========================================
>
>
> ------------------------------
>
> On Tue, Dec 18, 2018 at 10:49 AM Sri Prasanth Ghanta, Doctoral Research
> Scholar, Biosciences, SSSIHL <prasanthghanta at sssihl.edu.in> wrote:
>
>> Dear all,
>>
>> I have started following the new tutorial
>> <http://www.mdtutorials.com/gmx/complex/index.html> and the old tutorial
>> <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex_old/index.html>
>> to carryout the simulation of JZ4 with Lysozyme.
>> I was unable to run the cgenff script as I am not aware of setting up
>> microenvironment in Ubuntu to run older python version, which is essential
>> in running the script required for creation of ligand topology.
>>
>> From a bit of reading, I understood that ATBserver is preferred over
>> PRODRG as the topology created is more accurate.
>> I had followed the tutorial to build the complex (complex.gro) by
>> incorporating jz4.gro (from ATBserver) in the 3htb_processed.gro. I had
>> also incorporated the ligand topolgy (jz4.itp) into the topol.top as
>> instructed.
>> I was successful in building the box and solvating. However, when i try
>> to run
>> gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr
>> I get an error in line 1345 stating,
>> -----
>>
>> *Fatal error:*
>> *Atomtype CAro not found*
>>
>> *------*
>> I am assuming it's something to do with the representation of the carbon
>> (aromatic) in the topology of the ligand (jz4.itp), which reads like this..
>> -----------------------------------------
>> [ moleculetype ]
>> ; Name nrexcl
>> WX56 3
>> [ atoms ]
>> ; nr type resnr resid atom cgnr charge mass
>> 1 CH3 1 WX56 C1 1 -0.011 15.0350
>> 2 CH2 1 WX56 C2 2 0.028 14.0270
>> 3 CH2 1 WX56 C3 3 0.113 14.0270
>> 4 CAro 1 WX56 C4 4 -0.194 12.0110
>> 5 CAro 1 WX56 C9 5 0.338 12.0110
>> 6 OAlc 1 WX56 O1 6 -0.588 15.9994
>> 7 HS14 1 WX56 H12 7 0.428 1.0080
>> 8 CAro 1 WX56 C8 8 -0.268 12.0110
>> 9 HC 1 WX56 H11 9 0.167 1.0080
>> 10 CAro 1 WX56 C7 10 -0.100 12.0110
>> 11 HC 1 WX56 H10 11 0.131 1.0080
>> 12 CAro 1 WX56 C6 12 -0.201 12.0110
>> 13 HC 1 WX56 H9 13 0.136 1.0080
>> 14 CAro 1 WX56 C5 14 -0.124 12.0110
>> 15 HC 1 WX56 H8 15 0.145 1.0080
>> ; total charge of the molecule: -0.000
>> ------------
>>
>> However, I am not sure, which code I need to use in the place of CAro,
>> OAlc and HS14. Can you please help me in this regard?
>> P.S: I am trying to use GROMOS96 54a7 forcefield for this purpose.
>>
>> --
>> Regards,
>> Prasanth.
>>
>
>
> --
> Regards,
> Prasanth.
>
--
Regards,
Prasanth.
On Wed, Dec 19, 2018 at 3:05 PM Prasanth G, Research Scholar <
prasanthghanta at sssihl.edu.in> wrote:
> Dear Sir,
>
> I am running GROMACS 5.1.4 on a server.
> I had converted the protein(pdb2gro) using the latest GROMOS forcefield.
> As per your suggestion, I had downloaded the parameter files from ATB
> server. As per the readme file from the server (in the parameters folder),
> i had updated my topol.top like this and also included the extracted folder
> to the working directory on the server.
> ---
> ; Include Position restraint file
> #ifdef POSRES
> #include "posre.itp"
> #endif
>
> ; Include ligand topology
> #include "jz4.itp"
>
> ; Include force field parameters
> #include "home/bio1/PG/gromos54a7_atb.ff/forcefield.itp"
>
> ; Include topology for ions
> #include "home/bio1/PG/gromos54a7_atb.ff/ions.itp"
>
> ; Include water topology
> #include "home/bio1/PG/gromos54a7_atb.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
>
> [ system ]
> ; Name
> LYSOZYME
>
> [ molecules ]
> ; Compound #mols
> Protein_chain_A 1
> JZ4 1
> ------------
> However, when i try to execute the grompp to add ions, the error still
> persists-
>
> *Fatal error:*
>
> *Atomtype CAro not found *
>
> Could you please tell me, if i have to change the way this has to be
> done. Here is the list of parameter files obtained from the ATBserver.
> link- https://atb.uq.edu.au/molecule.py?molid=342699#panel-md
> ---
> aminoacids.c.tdb, aminoacids.hbd, amonoacids.n.tbb, aminoacids.r2b,
> aminoacids.rtp, aminoacids.vsd, atomtypes.atp, dppc.itp, ffbonded.itp,
> ffdum.itp, ffnonbonded.itp, forcefield.doc, forcefield.itp, ions.itp,
> popc.itp, README.md, spc.itp, spce.itp, tip3.itp, tip4.itp, tmcl.itp,
> watermodels.dat
> ---
>
> Thanks in advance,
> Prasanth.
>
> ----------------------------------------------------------------------------
> Are you trying to combine this ligand topology with the CHARMM protein
> topology generated in the tutorial? If so, that's fundamentally incorrect
> and you can never make that work.
>
> If you're doing things entirely within the context of GROMOS, then you
> likely need additional files from the ATB server that provide parameters
> for the "unknown" atom types.
>
> -Justin
> --
>
> ==========================================
>
> Justin A. Lemkul, Ph.D.
>
> Assistant Professor
>
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
>
> ==========================================
>
>
> ------------------------------
>
> On Tue, Dec 18, 2018 at 10:49 AM Sri Prasanth Ghanta, Doctoral Research
> Scholar, Biosciences, SSSIHL <prasanthghanta at sssihl.edu.in> wrote:
>
>> Dear all,
>>
>> I have started following the new tutorial
>> <http://www.mdtutorials.com/gmx/complex/index.html> and the old tutorial
>> <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex_old/index.html>
>> to carryout the simulation of JZ4 with Lysozyme.
>> I was unable to run the cgenff script as I am not aware of setting up
>> microenvironment in Ubuntu to run older python version, which is essential
>> in running the script required for creation of ligand topology.
>>
>> From a bit of reading, I understood that ATBserver is preferred over
>> PRODRG as the topology created is more accurate.
>> I had followed the tutorial to build the complex (complex.gro) by
>> incorporating jz4.gro (from ATBserver) in the 3htb_processed.gro. I had
>> also incorporated the ligand topolgy (jz4.itp) into the topol.top as
>> instructed.
>> I was successful in building the box and solvating. However, when i try
>> to run
>> gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr
>> I get an error in line 1345 stating,
>> -----
>>
>> *Fatal error:*
>> *Atomtype CAro not found*
>>
>> *------*
>> I am assuming it's something to do with the representation of the carbon
>> (aromatic) in the topology of the ligand (jz4.itp), which reads like this..
>> -----------------------------------------
>> [ moleculetype ]
>> ; Name nrexcl
>> WX56 3
>> [ atoms ]
>> ; nr type resnr resid atom cgnr charge mass
>> 1 CH3 1 WX56 C1 1 -0.011 15.0350
>> 2 CH2 1 WX56 C2 2 0.028 14.0270
>> 3 CH2 1 WX56 C3 3 0.113 14.0270
>> 4 CAro 1 WX56 C4 4 -0.194 12.0110
>> 5 CAro 1 WX56 C9 5 0.338 12.0110
>> 6 OAlc 1 WX56 O1 6 -0.588 15.9994
>> 7 HS14 1 WX56 H12 7 0.428 1.0080
>> 8 CAro 1 WX56 C8 8 -0.268 12.0110
>> 9 HC 1 WX56 H11 9 0.167 1.0080
>> 10 CAro 1 WX56 C7 10 -0.100 12.0110
>> 11 HC 1 WX56 H10 11 0.131 1.0080
>> 12 CAro 1 WX56 C6 12 -0.201 12.0110
>> 13 HC 1 WX56 H9 13 0.136 1.0080
>> 14 CAro 1 WX56 C5 14 -0.124 12.0110
>> 15 HC 1 WX56 H8 15 0.145 1.0080
>> ; total charge of the molecule: -0.000
>> ------------
>>
>> However, I am not sure, which code I need to use in the place of CAro,
>> OAlc and HS14. Can you please help me in this regard?
>> P.S: I am trying to use GROMOS96 54a7 forcefield for this purpose.
>>
>> --
>> Regards,
>> Prasanth.
>>
>
>
> --
> Regards,
> Prasanth.
>
--
Regards,
Prasanth.
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