[gmx-users] grompp error with gromacs-3.3

[Lei Zhou]

Hi,
thanks for the reply. I have removed those two 0's from the "imp" part and
now the grompp (of 3.3) is working. The modified ligand.itp is looks like
this:
3 1 4 13 2 35.3 334.8 35.3 334.8 ; imp C2* O2* C3* C1*
4 3 5 11 2 35.3 334.8 35.3 334.8 ; imp C3* C2* O3* C4*
....
13 3 1 2 1 0.0 1.3 3 0.0 1.3 3 ; dih C1* C2* O2* H8L
11 4 3 1 1 0.0 5.9 3 0.0 5.9 3 ; dih C4* C3* C2* O2*
....
I didn't do anything to the "dih" part. Is this correct, with two extra
columns representing "multi" for "dih" (3's shown above)?
 Another question is related with this. For the old grompp of 3.2.1, it
didn't give any warning about the extra "0"s for the impropers. Does this
affect the original MD results by 3.2.1?
 Thank you.
 Lei Zhou
Columbia University, NY

 On 10/16/05, David <spoel at xray.bmc.uu.se> wrote:
>
> On Sat, 2005-10-15 at 21:43 -0400, Lei Zhou wrote:
> > Hi,
> >
> > I am trying to use grompp in the recently released 3.3 to treat a
> > system of protein and ligand. However, with the same itp files used in
> > 3.2.1, there is error message saying that
> > ERROR 2 [file "ligand.itp", line 185]:
> > Too many parameters
> > ERROR 3 [file "ligand.itp", line 186]:
> > Too many parameters
> > ERROR 4 [file "ligand.itp", line 187]:
> > Too many parameters
> >
> > ...
> >
> > I checked that line and it contains information for dihedrals (made by
> prodrg webserver)
> > [ dihedrals ]
> > ; ai aj ak al fu c0, c1, m, ...
> > 3 1 4 13 2 35.3 334.8 0 35.3 334.8 0 ; imp C2* O2* C3* C1*
> >
> > 4 3 5 11 2 35.3 334.8 0 35.3 334.8 0 ; imp C3* C2* O3* C4*
>
> There shouldn't be a zero in the parameter section. The new grompp may
> be a bit stricter on checking the input. Impropers take two parameters
> only (plus two for FEP).
>
> >
> > Could you give me some suggestions? Thanks.
> >
> > Lei Zhou
> > Columbia University
> > New York, NY
> >
> >
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> --
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596, 75124 Uppsala, Sweden
> phone: 46 18 471 4205 fax: 46 18 511 755
> spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
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