[gmx-users] Protein-ligand complex simulation and ATBserver file

[Prasanth G, Research Scholar]

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.