[gmx-users] forcefield parameter missing

[Mark Abraham]

Hi,

Unfortunately, I don't know how/whether this worked in software that is a
decade old. Not too much has changed, however, so you may have better luck
(or error messages) with the most recent version, and thereby learn how to
get the topology to work.

Frankly, any force field that purportedly only works with 3.3.1 is likely
parameterized on model physics that were thought reasonable at the time,
but is now thought to be inferior to more recent integrators, algorithms or
implementations. And the performance will be atrocious compared to modern
versions. Switching force field, thereby obtaining higher sampling is a
serious option.

Mark

On Mon, May 15, 2017 at 11:55 AM Simon Kit Sang Chu <simoncks1994 at gmail.com>
wrote:

> 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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