Dear Lei,
This looks to me like xleap didn't even load the parm file and so doesn't
know about any atome types. E.g CT is a standard atom type.
Did you run leap with the command:
xleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff99
What lines of text were printed in the main xleap window when it first
appeared?
Ideally, what you want to do is create an frcmod file that contains your
extra parameters. Then you should load the unknown residue (from the pdb)
into Leap and edit the selected residue to set the atoms types, connectivity
and charges (you will need to run RESP) for the atoms in this new residue.
Then you can load the frcmod file and then solvate the system. In this way
you can avoid modifying the 'original' parm99.dat file.
For more details on creating your own residue you should refer to the
Plastocyanin tutorial.
http://amber.scripps.edu/tutorial/plastocyanin/pcy-tutorial.html
All the best
Ross
/\
\/
|\oss Walker
| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- ross.rosswalker.co.uk |
|
http://www.rosswalker.co.uk/ | PGP Key available on request |
> -----Original Message-----
> From: owner-amber.scripps.edu
> [mailto:owner-amber.scripps.edu] On Behalf Of lei jia
> Sent: 07 June 2004 15:13
> To: amber.scripps.edu
> Subject: AMBER: paramitrization problem
>
> Dear Amber Users,
>
> I am trying to paramitrize the force field (Amber7) for a special
> molecule. I added more than 10 new atom types, and bond lengths, bond
> angles, dihedral angles, impropers and vdw parameters corresponding to
> new atom types in the Parm99.dat. Then I added new atom types in the
> leaprc file. I had no problem to run xLeap and load my new molecule in
> with a Prep file. No parameters were missing But when I use
> 'solvatebox'
> to add water in the system. It can't give me the right radius for each
> atom.Instead, I got the warnings like this:
>
> > solvatebox a WATBOX216 2.0
> (using default radius 1.500000 for O3')
> (using default radius 1.500000 for C2')
> (using default radius 1.500000 for C3')
> (using default radius 1.500000 for O2)
> (using default radius 1.500000 for C2)
> (using default radius 1.500000 for N3)
> (using default radius 1.500000 for N4)
> (using default radius 1.500000 for C4)
> (using default radius 1.500000 for C5)
> (using default radius 1.500000 for C6)
> (using default radius 1.500000 for N1)
> (using default radius 1.500000 for C1')
> (using default radius 1.500000 for O4')
> (using default radius 1.500000 for C4')
> (using default radius 1.500000 for C5')
> (using default radius 1.500000 for O5')
> (using default radius 1.500000 for O3')
> (using default radius 1.500000 for O6)
> (using default radius 1.500000 for C6)
> (using default radius 1.500000 for N1)
> (using default radius 1.500000 for N2)
> (using default radius 1.500000 for C2)
> (using default radius 1.500000 for N3)
> (using default radius 1.500000 for C4)
> (using default radius 1.500000 for O5)
> (using default radius 1.500000 for C5)
> (using default radius 1.500000 for N7)
> (using default radius 1.500000 for O8)
> (using default radius 1.500000 for C8)
> (using default radius 1.500000 for N9)
> ....
>
> But actually Leap did add water in my system. When I tried to use
> 'saveAmberParm' to generate the topology file,it gave me such
> warnings:
>
> Building topology.
> Building atom parameters.
> For atom: .R<DC5 5>.A<H5T 1> Could not find type: HO
> For atom: .R<DC5 5>.A<O5' 2> Could not find type: OH
> For atom: .R<DC5 5>.A<C5' 3> Could not find type: CT
> For atom: .R<DC5 5>.A<H5'1 4> Could not find type: H1
> For atom: .R<DC5 5>.A<H5'2 5> Could not find type: H1
> For atom: .R<DC5 5>.A<C4' 6> Could not find type: CT
> For atom: .R<DC5 5>.A<H4' 7> Could not find type: H1
> For atom: .R<DC5 5>.A<O4' 8> Could not find type: OS
> For atom: .R<DC5 5>.A<C1' 9> Could not find type: CT
> For atom: .R<DC5 5>.A<H1' 10> Could not find type: H2
> For atom: .R<DC5 5>.A<N1 11> Could not find type: N*
> For atom: .R<DC5 5>.A<C6 12> Could not find type: CM
> For atom: .R<DC5 5>.A<H6 13> Could not find type: H4
> For atom: .R<DC5 5>.A<C5 14> Could not find type: CM
> For atom: .R<DC5 5>.A<H5 15> Could not find type: HA
> For atom: .R<DC5 5>.A<C4 16> Could not find type: CA
> For atom: .R<DC5 5>.A<N4 17> Could not find type: N2
> For atom: .R<DC5 5>.A<H41 18> Could not find type: H
> For atom: .R<DC5 5>.A<H42 19> Could not find type: H
> For atom: .R<DC5 5>.A<N3 20> Could not find type: NC
> For atom: .R<DC5 5>.A<O2 22> Could not find type: O
> For atom: .R<DC5 5>.A<C3' 23> Could not find type: CT
> For atom: .R<DC5 5>.A<H3' 24> Could not find type: H1
> .....
>
> It looks like the original atom types were not recognized.
> And topology
> file was not saved.Does anyone have experiences to
> parametrize the force
> field and tell me how to figure my problems out?I appreciate any
> suggestions.
>
> Lei Jia
>
>
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Received on Tue Jun 08 2004 - 08:53:01 PDT
