[gmx-users] Atomtype opls_236 not found

[Justin Lemkul]

On 1/31/19 11:48 PM, Anjali Patel wrote:
> Hello users,
>
> I know there are lots of discussion on this topic and i have gone through
> all those even whole chapter 5 also. but didn’t get any solution or where i
> am wrong. i want to generate .tpr file. i am using gmx grompp -f ions.mdp
> -c solv.gro -p topol.top -o ions.tpr. in that i have generated CNT topology
> file by this http://chembytes.wikidot.com/grocnt and molecule topology file
> taken by Automated topology builder (ATB) now i have merged both file and
> .top files is here,
>
> ; Include forcefield parameters
> #include "./cnt.ff/forcefield.itp"
>
> [ moleculetype ]
> ; Name            nrexcl
> CNT                 3
> [ atoms ]
> ;   nr       type  resnr residue  atom   cgnr     charge       mass
> typeB    chargeB      massB
>       1         CJ      1    UNK     C1      1          0     12.011   ;
> qtot 0
>       2         CJ      1    UNK     C2      2          0     12.011   ;
> qtot 0
>       3         CJ      1    UNK     C3      3          0     12.011   ;
> qtot 0
>       4         CJ      1    UNK     C4      4          0     12.011   ;
> qtot 0
>    .......
>
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ;  i funct       fcx        fcy        fcz
>     1    1       1000       1000       1000
> #endif
>
> ; Include forcefield parameters
> #include "./oplsaa.ff/forcefield.itp"
>
> ; Include ligand topology
> #include "drug.itp"
>
> ; Include topology for ions
> #include "./oplsaa.ff/spc.itp"
>
> ; Include water topology
> #include "oplsaa.ff/tip3p.itp"
>
> [ system ]
> ; Name
> CNT in water
>
> [ molecules ]
> ; Compound        #mols
> CNT               1
> _JDN               1
> SOL              2515
>
> where drug.itp is below
>
>
> ; Include forcefield parameters
> #include "./oplsaa.ff/forcefield.itp"
>
> [ moleculetype ]
> ; Name            nrexcl
> _JDN                3
>
> [ atoms ]
> ;   nr       type  resnr residue  atom   cgnr     charge       mass
> typeB    chargeB      massB
>       1   opls_236      0   _JDN    O14      0     -0.500
> 15.99940
>       2   opls_145      0   _JDN    C41      1      0.000
> 12.01100
>       3   opls_145      0   _JDN    C42      2      0.000
> 12.01100
>       4   opls_145      0   _JDN    C47      3     -0.115
> 12.01100
>       5   opls_146      0   _JDN    H51      3      0.115
> 1.00800
> ............
>
> opls_236 and all atom types are already in .rtp, .atp and ffnonbonded.itp
> file. i am not getting the issue. as it is very urgent for me
>
> Thanks in advance for any advice and suggestions

You're mixing force fields. You've got one component that uses OPLS-AA 
and one that comes from ATB, which produces GROMOS-compatible 
topologies. You're even trying to #include multiple force fields. This 
approach is fundamentally incorrect. You need to use one force field to 
describe all the components of your system.

-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

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