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

[한상화]

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.

 

Sanghwa Han

 

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