[gmx-users] forcefield parameter missing

[Simon Kit Sang Chu]

Hi Mark,

The complete story was to add a manually capped residue for VAL and I named
it as VAT. NH2 capped was borrowed from NH2 in residue ASN. I hope to
borrow the parameters from ASN to VAT too but then the error comes.

To add the new residue VAT, I have included it in aminoacids.dat
(gromacs3.3.1), ffPACE_1.3.rtp and ffPACE_1.3.hdb. The atom types and names
are all borrowed from ASN. The forcefield implementation strictly requires
gromacs3.3.1 and I have to add the capping manually.

The output seems well. Most of them are of the same problem I mentioned
previously - failed to recognize the existing parameters. The first 8
errors are of this type.

checking input for internal consistency...
calling cpp...
processing topology...
Generated 2819 of the 4371 non-bonded parameter combinations
WARNING 1 [file "P1tail-pace.top", line 825]:
  No default LJ-14 types, using zeroes
WARNING 2 [file "P1tail-pace.top", line 826]:
  No default LJ-14 types, using zeroes
WARNING 3 [file "P1tail-pace.top", line 827]:
  No default LJ-14 types, using zeroes
WARNING 4 [file "P1tail-pace.top", line 828]:
  No default LJ-14 types, using zeroes
WARNING 5 [file "P1tail-pace.top", line 829]:
  No default LJ-14 types, using zeroes
WARNING 6 [file "P1tail-pace.top", line 830]:
  No default LJ-14 types, using zeroes
WARNING 7 [file "P1tail-pace.top", line 831]:
  No default LJ-14 types, using zeroes
WARNING 8 [file "P1tail-pace.top", line 1532]:
  No default LJ-14 types, using zeroes
WARNING 9 [file "P1tail-pace.top", line 1539]:
  No default Angle types, using zeroes
WARNING 10 [file "P1tail-pace.top", line 2113]:
  No default Proper Dih. types, using zeroes

Hopefully this adds a bit more clue.

Regards,
Simon

2017-05-15 17:42 GMT+08:00 Mark Abraham <mark.j.abraham at gmail.com>:

> Hi,
>
> It's hard to tell from this fragment. Are your include files all what you
> think they are? Does grompp terminal output all make sense?
>
> Mark
>
> On Mon, May 15, 2017 at 10:43 AM Simon Kit Sang Chu <
> simoncks1994 at gmail.com>
> wrote:
>
> > Hi everyone,
> >
> > I need to add a new residue in my forcefield and borrow the atoms and
> > parameter from another existing residue. I encounter missing parameter
> > warning for a number of bonds. However, if I check in .itp, the
> parameters
> > exist. Is there something I missed?
> >
> > Here is an example I encounter.
> >
> >
> > *Warning*
> >
> > WARNING 1 [file "P1tail-pace.top", line 824]:
> >           No default LJ-14 types, using zeroes
> >
> > *P1tail-pace.top*
> >
> > [ exclusions ]
> > [ pairs ]
> > ;  ai    aj funct            c0            c1            c2            c3
> >
> >     1     7     1
> >                *  line 827*
> >
> >
> > *P1tail-pace.top*
> >
> > [ atoms ]
> > ;   nr       type  resnr residue  atom   cgnr     charge       mass
> typeB
> >    chargeB      massB
> >      1         NT      1    VAT    ND2      1          0          6   ;
> > qtot 0
> > .
> > .
> > .
> >      7          O      1    VAT      O      4          0         16   ;
> > qtot 0
> >
> > *ffPACE_1.3.itp*
> > [ nonbond-params ]
> > O  NT    1   0.0    1.70202E-06
> >
> >
> > I appreciate any suggestion or help.
> >
> > Regards,
> > Simon
> > --
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