AMBER Archive (2009)

Subject: Re: [AMBER] database

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Fri Sep 18 2009 - 02:28:53 CDT

Quoting case <case_at_biomaps.rutgers.edu>:

ok & thank you for the help.

It looks like it appends using the OFF file format as well. This is
not only related to the Tripos mol2 file format.

regards, Francois

> On Thu, Sep 17, 2009, Steve Seibold wrote:
>>
>> I made all atom names unique, but identical in mol2 and pdb files. I
>> took this pdb file (with identical *unique* mol2 names) and opened
>> the pdb file in VMD without any problems and then resaved it as pdb
>> file. The thinking is that now it (the pdb file) would be written
>> correctly. (VMD did not change the sequence or names of the atoms and
>> still treated the molecule as three residues.)Again leap failed to
>> coordinate atom types with the pdb file.
>
> OK: I think I see your problem.
>
> The mol2 file attempts to use the tripos "SUBSTRUCTURE" command
> to define four residues, named "P2M", "P1", "P1" and "C5". But the Amber
> loadMol2 commnad doesn't truly use this information in the way one might
> expect. When you say
>
> FOO = loadpdb dCTP2.mol2
>
> you will get *one* unit, named "FOO", with 40 atoms in it. Using the
> "list" and "desc" commands shows that it indeed consists of 4 residues
> (with names like that in the pdb), but it is unit name that leap uses to
> match residue names in the pdb file. Bascially, "loadMol2" can be used to
> load a single residue at a time, not multiple residues.
>
> The PDB file looks like a single triphosphate molecule (albeit with
> a bad bond
> length between the second and third phosphates.) I suggest that you make
> the mol2 file as a single residue, and change the PDB file appropriately.
>
> [Aside: sleap handles this a little better: it gives a somewhat more
> informative set of error messages; but it does essentially the same thing:
>
> poincare% sleap
> [gtkleap]$ source leaprc.ff99SB
> [gtkleap]$ FOO = loadmol2 dCTP2.mol2
> [gtkleap]$ x = loadpdb newdCTP3.pdb
> Warning: cannot find template for residue P2M in our library.
> You will not be able to save prmtop for this molecule.
> Warning: cannot find template for residue P2M in our library.
> You will not be able to save prmtop for this molecule.
> Warning: cannot find template for residue P1 in our library.
> You will not be able to save prmtop for this molecule.
> Warning: cannot find template for residue P1 in our library.
> You will not be able to save prmtop for this molecule.
> Warning: cannot find template for residue C5 in our library.
> You will not be able to save prmtop for this molecule. ]
>
> ...dac

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