[gmx-users] Error in top when using oplsaa with tip4p

[David van der Spoel]

한상화 wrote:
> Dear colleagues,
> 
>  
> 
> I carried out successfully an MD simulation of a protein in water using 
> the GROMOS 96 force field with spce water.
> 
> But I have a problem in switching to OPLSaa.
> 
> I proceeded as usual:
> 
> # pdb2gmx -ff oplsaa -f pn.pdb -o pn2.pdb -p pn.top -his -ss –water tip4p
> 
> # editconf -bt octahedron -f pn2.pdb -o pn3.pdb -c -d 1.0
> 
> # genbox -cp pn3.pdb -cs tip4p.gro -o pn_em.pdb -p pn.top
> 
> # grompp -f em.mdp -c pn_em.pdb -p pn.top -o pn_em.tpr
> 
>  
> 
> At this stage, I received an error message:
> 
> ===============================================================
> 
> checking input for internal consistency...
> 
> calling /usr/bin/cpp...
> 
> processing topology...
> 
> Generated 332520 of the 332520 non-bonded parameter combinations
> 
> Generating 1-4 interactions: fudge = 0.5
> 
> Generated 332520 of the 332520 1-4 parameter combinations
> 
> Excluding 3 bonded neighbours for Protein 1
> 
> Excluding 2 bonded neighbours for SOL 36
> 
> Excluding 2 bonded neighbours for SOL 4710
> 
> NOTE:
> 
>   System has non-zero total charge: -5.000000e+00
> 
>  
> 
> processing coordinates...
> 
> -------------------------------------------------------
> 
> Program grompp, VERSION 3.3.1
> 
> Source code file: grompp.c, line: 448
> 
>  
> 
> Fatal error:
> 
> number of coordinates in coordinate file (pn_em.pdb, 20758)
> 
>              does not match topology (pn.top, 20614)
> 
> -------------------------------------------------------
> 
> ===============================================================
> 
>  
> 
> So I checked the pn_em.pdb and found that 4782 water molecules were 
> added. However, at the end of pn.top it says:
> 
> ====================
> 
>  [ molecules ]
> 
> ; Compound        #mols
> 
> Protein             1
> 
> SOL                36
> 
> SOL              4710
> 
> ====================
> 
>  
> 
> I do not understand why there are two classes of solvents.
> 
>  
> 
> Anyway, I changed the number of SOL in pn.top to 4782 and run grompp 
> again. But this time I get the following warning:
> 
> =================================================================
> 
> processing coordinates...
> 
> Warning: atom names in pn.top and pn_em.pdb don't match (MW - HW3)
> 
> Warning: atom names in pn.top and pn_em.pdb don't match (MW - HW3)
> 
> Warning: atom names in pn.top and pn_em.pdb don't match (MW - HW3)
> 
> Warning: atom names in pn.top and pn_em.pdb don't match (MW - HW3)
> 
> Warning: atom names in pn.top and pn_em.pdb don't match (MW - HW3)
> 
> Warning: atom names in pn.top and pn_em.pdb don't match (MW - HW3)
> 
> Warning: atom names in pn.top and pn_em.pdb don't match (MW - HW3)
> 
> Warning: atom names in pn.top and pn_em.pdb don't match (MW - HW3)
> 
> Warning: atom names in pn.top and pn_em.pdb don't match (MW - HW3)
> 
> Warning: atom names in pn.top and pn_em.pdb don't match (MW - HW3)
> 
> Warning: atom names in pn.top and pn_em.pdb don't match (MW - HW3)
> 
> Warning: atom names in pn.top and pn_em.pdb don't match (MW - HW3)
> 
> Warning: atom names in pn.top and pn_em.pdb don't match (MW - HW3)
> 
> Warning: atom names in pn.top and pn_em.pdb don't match (MW - HW3)
> 
> Warning: atom names in pn.top and pn_em.pdb don't match (MW - HW3)
> 
> Warning: atom names in pn.top and pn_em.pdb don't match (MW - HW3)
> 
> Warning: atom names in pn.top and pn_em.pdb don't match (MW - HW3)
> 
> Warning: atom names in pn.top and pn_em.pdb don't match (MW - HW3)
> 
> Warning: atom names in pn.top and pn_em.pdb don't match (MW - HW3)
> 
> Warning: atom names in pn.top and pn_em.pdb don't match (MW - HW3)
> 
> (more than 20 non-matching atom names)
> 
> WARNING 1 [file "pn.top", line 15315]:
> 
>   36 non-matching atom names
> 
>   atom names from pn.top will be used
> 
>   atom names from pn_em.pdb will be ignored
> 
> =================================================================
> 
>  
> 
> Everything was OK with GROMOS 96 and spce water.
> 
> Any suggestions would be greatly appreciated.
> 
you solved the problem.

-- 
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se