AMBER Archive (2009)

Subject: RE: [AMBER] database

From: Steve Seibold (seibold_at_chemistry.msu.edu)
Date: Fri Sep 18 2009 - 10:03:44 CDT

Thanks much Prof Case and Franscois for your comments. I have made my newCTP2.mol2 into one residue and opened it up to verify this in leap. I then once again tried to open my newdCTP3.pdb to match atom types. Once again it failed. None of the atoms were recognized same as before.

Not to be discouraged, I then took my PDB file and opened it up in a software package that writes mol2 files. I took the PDB (my newdCTP3.pdb) and made a mol2 file of this newCTP3.pdb using this software. I then opened the mol2 file (containing the correct atom types OS..etc same as before) in leap with no problem. It was one residue etc. I then tried again to use leap to assign atom types to my newdCTP3.pdb file. Again, none of the atoms were recognized.

I am using AMBER8 (hoping to get the newer version soon). Does this make a difference?

Steve

-----Original Message-----
From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On Behalf Of case
Sent: Thursday, September 17, 2009 6:24 PM
To: AMBER Mailing List
Subject: Re: [AMBER] database

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

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber



  • application/octet-stream attachment: leap.in


_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber