AMBER Archive (2009)

Subject: RE: [AMBER] database

From: Steve Seibold (seibold_at_chemistry.msu.edu)
Date: Thu Sep 17 2009 - 14:46:20 CDT

Hi Francois
Thanks for your help and I truly hope it is not an inconvenience but, here is what I have done:

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.

I then went to the official PDB format web site and formatted my PDB (newdCTP3.pdb) using their rules. I have the comparison in the file (attached). The first three lines are copied from that web site to show that the newdCTP3.pdb file is in compliance.
I then again ran "leap.in" and it again failed. The interesting thing is that not even *one* atom was recognized! In fact, I get the same error if I only load the pdb without any parameter files present.

I then took (from AMBER's web site) frmcod and prepi files for another ligand I have to see if leap worked with them and there was no problem. Leap opened up the prep files and my ligand.pdb assigned atom types.

I am at a loss as to what to try next..?

Thanks, Steve

Steve Seibold
Research Asst. Professor
seibold_at_chemistry.msu.edu
19B Chemistry Building
Michigan State University
East Lansing, MI 48824
Office 517-355-9715 ext 264
 

-----Original Message-----
From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On Behalf Of FyD
Sent: Thursday, September 17, 2009 12:00 PM
To: AMBER Mailing List
Subject: RE: [AMBER] database

Steve,

> I have been attempting to load the pdb file which, as you can see in
> the attachment is identical in residues, atom names to the mol2
> file and still I am getting the error in leap saying it does not
> have atom types for my pdb. I have also attempted with "TER" and in
> its absence to no success.

The residue name & atom names have to be identical in the PDB and mol2 files.
Thus, this is normal it does not work.

The residue names in the mol2 file are: P2M P1 P1 & C5
The residue names in the PDB file are: PM2 P1 P1 & C5
Moreover, there are errors in the residue name (shift & empty character).
Check also for putative inversion in atom names (for instance H11
which becomes 1H1).

> I hope I am not doing something dumb and wasting your time. I am
> sending you everything I am using. Can you give it a glance and tell
> me if you have any ideas?

See above & below.

> Is the problem that these mol2 files were not made with gaff.dat/antechamber?
> Is there a way to convert mol2 files to prepi files if necessary or
> would this even help?

I think this is a general problem of FF library recognition.

regards, Francois

Below is wrong:
REMARK
HETATM10305 OR PM2 A 201 46.999 35.394-110.730 1.00 32.71 O
HETATM10306 P PM2 A 201 48.402 34.814-111.258 1.00 32.34 P
HETATM10307 OP1 PM2 A 201 48.870 33.764-110.316 1.00 33.57 O
HETATM10308 OP2 PM2 A 201 48.292 34.479-112.691 1.00 33.25 O
TER
HETATM10309 OP3 PM2 A 202 49.362 36.087-111.126 1.00 32.50 O
HETATM10301 OR P1 A 202 44.930 34.458-111.161 1.00 29.92 O
HETATM10302 P P1 A 202 45.783 35.734-111.732 1.00 31.42 P
HETATM10303 OP1 P1 A 202 44.906 36.821-111.230 1.00 30.92 O
HETATM10304 OP2 A 202 45.895 35.340-113.143 1.00 32.96 O
etc...

It should be as in the mol2 file, i. e.:
REMARK
HETATM10305 OR P2M A 201 46.999 35.394-110.730 1.00 32.71 O
HETATM10306 P P2M A 201 48.402 34.814-111.258 1.00 32.34 P
HETATM10307 OP1 P2M A 201 48.870 33.764-110.316 1.00 33.57 O
HETATM10308 OP2 P2M A 201 48.292 34.479-112.691 1.00 33.25 O
HETATM10309 OP3 P2M A 201 49.362 36.087-111.126 1.00 32.50 O
TER
HETATM10301 OR P1 A 202 44.930 34.458-111.161 1.00 29.92 O
HETATM10302 P P1 A 202 45.783 35.734-111.732 1.00 31.42 P
HETATM10303 OP1 P1 A 202 44.906 36.821-111.230 1.00 30.92 O
HETATM10304 OP2 P1 A 202 45.895 35.340-113.143 1.00 32.96 O
etc...

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