Dear David and Dan,
Thanks for your suggestions!
It became more clear to me when I discovered the possibility to work with saveoff/loadoff bla.lib... So, you do once everything until the rise of an indication of your problem, then you save the parameters (saveoff mol mol.lib), close down tleap, and start tleap again to read in (loadoff) mol.lib.
In this .lib file, you can then also check with a text editor the name of the residu and verify whether it is the same in your pdb file... After a fix (in my case "0" is indeed a quite unconventional or difficult name - and list and desc are nice tools when you have naming issues), the problem can be solved :-).
Bye,
Stefan
________________________________________
From: David A Case [case.biomaps.rutgers.edu]
Sent: 24 January 2013 15:41
To: AMBER Mailing List
Subject: Re: [AMBER] Problem compatibility pdb in tleap
On Thu, Jan 24, 2013, Stefan Knippenberg wrote:
>
> Thanks for your suggestion about using ptraj via rst and then ambpdb,
> but it does not help.
>
> There is probably an issue the way I mention the .mol2 for the
> non-standard residu in tleap. Is it enough to say "loadmol2
> mol.mol2"? What don't I understand here?
>
> tleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff99SB
> mol = loadmol2 mol.mol2
> loadamberparams test.frcmod
> gaff = loadamberparams gaff.dat
> complex = loadpdb test.pdb
The "list" and "desc" commands should help. Use "list" to find out what tleap
thinks the residue names are, and "desc" to poke around inside those.
>
> and then we get:
>
> Created a new atom named: H within residue: .R<0 1>
You still seem to have a residue named "0" in your pdb file; is this really
what the residue is called in your previous prmtop file? Is it what the
residue is called in the mol2 file?
The message above says that there is an atom in the pdb file (residue
name/atom name pair) that does not exist in any library you have loaded. By
whatever means necessary, you have to make the pdb file names match those in
the libraries.
...dac
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Received on Thu Jan 24 2013 - 10:30:02 PST
