Dear Ben,
- In a given residue in a force field library two atoms cannot shares
the same name (while chemical elements can be used as atom names when
one only wants to display a PDB file in a graphical program).
- In a force field library two equivalent atoms should bear the same
charge value.
- A P2N file is a PDB file with two columns of atom names; the first
one reflecting chemical equivalencing (yellow column in the example
below) and the second one (red column in the example below) containing
the real atom names of the force field library to be buit. See an
example with 2 conformations .
http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#EXAMPLE-P2N-FILE
- Ante_R.E.D. generates P2N file(s) from PDB file(s), and R.E.D. uses
P2N file(s) to generate mol2 file(s) (the force field library file
format generated by R.E.D.).
- Ante_R.E.D. 1.x from the R.E.D. tools at
http://q4md-forcefieldtools.org/RED/ just uses a PDB file as input and
generates a P2N file, but does NOT check for errors (duplicated atom
names for instance) in the PDB input file. Ante_R.E.D. 1.x does not
know how to deal with chemically equivalent atoms in different group
of atoms. Thus, a user has to manually check the P2N file generated by
Ante_R.E.D. 1.x. This is quite painful when the molecule is large...
Ante_R.E.D. 2.0 interfaced by R.E.D. Server performs many checking
and its goal is to correct all the errors in an input PDB file when
one targets to build a force field library. Thus, Ante_R.E.D. 2.0
corrects duplicated atom names and deals with chemical equivalencing.
See
http://q4md-forcefieldtools.org/REDS/news.php
http://q4md-forcefieldtools.org/REDS/news.php#2
You can also see a complex example of chemical equivalencing in the
R.E.D. Server tutorial .
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php.
(thanks to Alan Wilter for providing this molecule; P2N file generated
by Ante_R.E.D. 2.0). See the Java applet:
http://q4md-forcefieldtools.org/Tutorial/P2N/Complex-equiv/javaappletpdb-1.html
My guess is that if you have a problem of atom names in your force
field library you used Ante_R.E.D. 1.x. Try using Ante_R.E.D. 2.0 to
generate your P2N file, or send us your PDB input file, P2N file and
mol2 file.
Several comments below in your email... I hope this helps.
regards, Francois
PS: You do not need to transform a mol2 file into OFF .lib file as
both file formats have the same 'role' in LEaP: a force field library
file format; you might also be interested by the .mol3 file format we
are developing in LEaP;
see
http://q4md-forcefieldtools.org/Tutorial/leap-mol3.php
Quoting Ben Ahmady <uccabha.ucl.ac.uk>:
> My question - as per the subject title - relates in part to the R.E.D.
> Server; however, as I am ultimately going to want to attempt to work
> with AMBER 11/AmberTools 1.5 (specifically: Antechamber), I am posting
> my question here rather than on the R.E.D. Server's list.
>
> Firstly, what I want to do is to take the RESP-derived charges I have
> for ethyl phosphate and create a topology file for it.
>
> I have followed the guidelines set out by the R.E.D. team on their
> website and have managed to obtain a mol2 file for ethyl phosphate
> (etp.mol2). Running parmchk on this as follows ...
>
> parmchk -i etp.mol2 -f mol2 -o etp.frcmod
- You can easily add force field atom types manually in the mol2 file
format generated by R.E.D.
- For ethylphosphate I do not think you need a frcmod file...
> ... suggests (I looked at the frcmod file) that there are missing
> parameters for 'MASS', 'BOND', 'ANGLE', 'DIHE', 'IMPROPER', and 'NONBON'.
>
> Using Ross Walker's tutorial
> (http://ambermd.org/tutorials/basic/tutorial4b/) as my framework I ran
> the following:
>
> tleap -f leaprc.ff99SB
> source leaprc.gaff
> ETP = loadmol2 etp.mol2
>
> ... so far so good. Moving on:
>
> check ETP
>
> ... this suggests that "there are missing parameters", which makes sense
> given the output of parmchk and the contents of Ross Walker's tutorial.
> Fine.
Missing force field parameters for ethylphosphate? this is strange: I
might be wrong but it looks like to me this is very unlikely...
Did you load of force field parameter file such as parm99.dat in LEaP?
Did you add the force field atom types in the mol2 file generated by R.E.D.?
See
http://q4md-forcefieldtools.org/REDDB/projects/F-90/
http://q4md-forcefieldtools.org/REDDB/projects/F-90/script1.ff
set P2M name "P2M"
...
set P2M.1 restype undefined
set P2M.1 name "P2M"
# set FF atom types
set P2M.1.OR type OS
set P2M.1.P type P
set P2M.1.OP1 type O2
set P2M.1.OP2 type O2
set P2M.1.OP3 type O2
-> you need to define the FF atom types for the ethyl group...
CT, HC, HC, HC, CT, H1, H1
> Moving on:
>
> loadamberparams etp.frcmod
> saveoff ETP etp.lib
saveoff is useless because OFF and mol2 file formats are both a force
field library file format.
> saveamberparm ETP etp.prmtop etp.inpcrd
>
> Nothing obviously wrong so far. So then I went out of tleap and went
> back in:
>
> tleap -f leaprc.ff99SB
> source leaprc.gaff
> loadamberparams etp.frcmod
> loadoff etp.lib
>
> Then, I tried to run:
>
> pdb = loadpdb etp.pdb
>
> But was alerted to the fact that some of my atom names weren't unique in
> 'etp.pdb', so I set about changing that according to convention (making
> sure not to disturb any of the spacing); however, these didn't match
> those in the P2N file which was generated by R.E.D since it is apparent
> to me that the P2N accepts duplicate atom names on the basis of atom
> equivalence and I am given to believe that the PDB does not (at least in
> this context).
See explanations above
> In any case, after fixing the above I then ran all of the
> above commands again leading up to the last one, which I modified
> slightly (calling it 'ethylphosphate' as opposed to 'pdb'):
>
> ethylphosphate = loadpdb etp.pdb
>
> At first it seemed to be working and was giving output along the lines
> of ...
>
> Created a new atom named: CT1 within residue: .R<ETP 0>
Error here: a CT1 atom name should not be present in the unique column
of atom name of the PDB file format...
> Created a new atom named: O2 within residue: .R<ETP 0>
> Created a new atom named: P3 within residue: .R<ETP 0>
> Created a new atom named: O4 within residue: .R<ETP 0>
>
> ... but then it suddenly gave the following error message:
>
> Bond: Maximum coordination exceeded on .R<ETP 0>.A<H1 14>
> -- setting atoms pert=true overrides default limits
> ATOMS NOT BONDED: .R<ETP 0>.A<CT1 15> .R<ETP 0>.A<H1 14>
> !FATAL ERROR----------------------------------------
> !FATAL: In file [atom.c], line 444
> !FATAL: Message: bondAtomProblem found
> !
> !ABORTING.
>
> ... I realise that other AMBER users have had similar sorts of problems
> before (as evidenced by some e-mails in the mailing list archive) but
> having read the responses I haven't been able to find anything that
> actually helps me fix this problem, and as a new computational chemistry
> PhD I don't have enough of an idea about how to implement 'atoms
> pert=true'. As a result any help would be greatly appreciated.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Jan 06 2012 - 01:00:02 PST
