[gmx-users] Re: Problem in adding Ryckaert-Bell. types using charmm

[Mark Abraham]

sarbani chattopadhyay wrote:
>   Respected Sir,
>                       I am facing a problem while trying to run gromacs 
> using charmm.

Please keep GROMACS-related questions on the users mailing list. This 
way the answers are archived for other people, and you get the ability 
for multiple people to consider helping with your problem.

>   I proceedwed in the following way:
> pdb2gmx -f str.pdb -ff oplsaa -ter -o opls.gro
> 
> pdb2gmx -f opls.gro -ff charmm -ter

You do not need two steps here. pdb2gmx -f str.pdb -ff charmm -ter is 
all you need.

> output -> conf.gro
>           posre.itp
>           topol.top
>          
> charmm27-run-addtop-gromacs-dihe.sh topol.top new.top

I do not provide support for using this script since I didn't write it.

If you use my perl script for converting your CHARMM .prm file, and then 
  pdb2gmx using a suitable .rtp file (e.g. from Yuguang Mu's pacakge), 
and then my perl script for fixing the grompp warnings, then you should 
be OK.

> mv topopl.top prev_topol.top
> 
> mv new.top topol.top
> 
> editonf -f conf.gro -bt cubic -d 0.75 -bt cubic -o box.gro
> 
> genbox -cp box.gro -cs spc216.gro -p topol.top -o wid-water.gro
> 
> grompp -f em.mdp -c wid-water.gro -o em.tpr
> 
> xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
> 
> ERROR
> 
> topol.top:630:29: warning: missing terminating ' character
> processing topology...
> Generated 0 of the 8646 non-bonded parameter combinations
> ERROR 0 [file "topol.top", line 533]:
>   No default Ryckaert-Bell. types
> Excluding 3 bonded neighbours for Protein 1
> Excluding 1 bonded neighbours for SOL 455
> removed 53 distance restraints
> processing coordinates...
> double-checking input for internal consistency...
> renumbering atomtypes...
> converting bonded parameters...
> #      BONDS:  59
> #    ANGLES:  108
> #      PDIHS:  50
> #    RBDIHS:  125
> #      LJ14:  150
> #    SETTLE:  455
> 
> -------------------------------------------------------
> Program grompp, VERSION 3.3.2
> Source code file: grompp.c, line: 1182
> 
> Fatal error:
> There was 1 error in input file(s)
> -------------------------------------------------------
> xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
> 
> Using  fix_top_for_charmm.pl on topol.top gives the following statement
> 
> Success! .top file did not need fixing for CHARMM forcefield.   
> 
> If you give me some suggestions on how to solve this problem I will be 
> highly obliged.

See above, or please provide your fix_top_for_charmm.pl command line.

Mark