AMBER Archive (2009)

Subject: RE: [AMBER] database

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Thu Sep 17 2009 - 16:54:29 CDT

Steve,

May I ask you to send me (to my personal email address) your protein
complex with dCTP in the PDB file format so that I can play with it.

regards, Francois

> 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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>

           F.-Y. Dupradeau
                 ---
http://q4md-forcefieldtools.org/FyD/

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