Dear AMBER Users/Developers
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
... 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. Moving on:
loadamberparams etp.frcmod
saveoff ETP etp.lib
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). 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>
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.
Best wishes
Ben Ahmady
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Received on Thu Jan 05 2012 - 10:00:03 PST
