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

[Sri Prasanth Ghanta, Doctoral Research Scholar, Biosciences, SSSIHL]

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.