[gmx-users] Re: .top file incoherent with the values in the ffbonded.itp file
Justin A. Lemkul
jalemkul at vt.edu
Sat Jun 30 01:10:12 CEST 2012
On 6/29/12 6:10 PM, sreeta.g wrote:
> Hi Justin
> I have changed all the force field parameters as below, (I have already
> shown my ffbonded.itp file)
> ; name bond_type mass charge ptype sigma epsilon
> opls_966 CA 6 12.01100 0.240 A 3.5000e-01
> opls_967 CA 6 12.01100 0.180 A 3.5000e-01
> opls_968 HB1 1 1.00800 0.060 A 2.5700e-01
> opls_969 HB2 1 1.00800 0.060 A 2.5700e-01
> opls_970 HB3 1 1.00800 0.060 A 2.5700e-01
> opls_971 HA1 1 1.00800 0.060 A 2.5700e-01
> opls_972 HA2 1 1.00800 0.060 A 2.5700e-01
> C opls_136 -0.120 12.011 4 C 0.153 H 0.11 H 0.110 H 0.110
> C opls_966 0.240 12.011 4 C 0.153 H 0.11 H 0.110 O 0.143
> C opls_135 -0.180 12.011 4 C 0.153 H 0.11 H 0.110 H 0.110
> O opls_154 -0.700 15.999 2 C 0.143 H 0.097
> [ Pva ]
> [ atoms ] ; see atomtypes.atp for explainations
> CB opls_136 -0.120 1
> HB1 opls_968 0.060 1
> HB2 opls_969 0.060 1
> CA opls_966 0.240 2
> ..... (contd)
> so I have maintained consistency in my atom types in the ffbonded.itp files.
> When I am running Grompp, it gives 7988 errors and I have 9088 atoms in my
> polymer chain. All the errors mentioned are No default Ryckaert-Bell. types,
> which I explained to you in my first mail.
> So I am still unsure as to what my problem is and how I should deal with it.
The only way to diagnose the problem is to check your self-consistency.
Probably most of the errors are redundant. Choose one of them (it tells you the
line where the error occurs), write down the atom numbers involved and then look
up which atom types (not names) to which these numbers pertain. That is the
missing interaction type that needs to be defined in ffbonded.itp.
I can't tell what's wrong based on the snippets of files shown. You can, based
on having a very careful look through all of your files.
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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