Hello,
I have encountered a problem in the
loadpdb execution of tleap. I am trying to generate prmtop and prmcrd
files for a molecular triad composed of Carotenoid-Porphyrin-C60
subunits. Before attempting antechamber/tleap runs for the triad, I am
working on each of the three subunits separately. Consequently, I have
successfully generated prep and frcmod files for each component with the
use of antechamber. Next, the following script (leap.in) was run with
tleap (./tleap -s -f leap.in) for a C60-pyrolle molecule.
%%%
antechamber command used: ./antechamber -i Frag_C60-pyrolle.pdb -fi
pdb -o Frag_C60-pyrolle.prep -fo prepi -c gas -j 4 -at gaff -du y
%%% parmchk command used: ./parmchk -i Frag_C60-pyrolle.prep -f prepi -o Frag_C60-pyrolle.frcmod -p gaff.dat -w Y
leap.in:
LoadAmberParams gaff.dat
LoadAmberParams Frag_C60-pyrolle.frcmod
LoadAmberPrep Frag_C60-pyrolle.prep
sys = loadpdb NEWPDB.PDB
saveAmberParm sys C.top C.crd
quit
I
looked extensively through the amber archives and encountered several
discussions closely related to the error message that I receive and will
display below. From what I understand, the pdb file loaded by tleap
through the loadpdb command does not make use of the atom types
corresponding to the gaff force field atom types (such as those
displayed in the prep file). In fact, tleap states that the atom names
should be unique for each residue. In my case, the entire C60-pyrolle
molecule is one residue. I have attached 2 different input pdb files
that I ran in tleap (NEWPDB.PDB and Test.pdb), the prep file, and the
frcmod file. In addition, I have attached a log file (tleap.log)
containing the entire error message given by the tleap program since
below is included only an excerpt. Thank you very much for your time.
Any suggestions would be greatly appreciated.
Regards,
Marco Olguin
Graduate Student
University of Texas at El Paso
Error Message:
Welcome to LEaP!
Sourcing: ./leap.in
Loading parameters: ./gaff.dat
Reading title:
AMBER General Force Field for organic molecules (Version 1.4, March 2010) add. info. at the end
Loading parameters: ./Frag_C60-pyrolle.frcmod
Reading force field modification type file (frcmod)
Reading title:
remark goes here
Loading Prep file: ./Frag_C60-pyrolle.prep
Loading PDB file: ./NEWPDB.PDB
Unknown residue: number: 0 type: Terminal/last
..relaxing end constraints to try for a dbase match
-no luck
Creating new UNIT for residue: sequence: 0
Created a new atom named: C25 within residue: .R< 0>
Created a new atom named: C7 within residue: .R< 0>
Created a new atom named: C22 within residue: .R< 0>
Created a new atom named: C5 within residue: .R< 0>
Created a new atom named: C23 within residue: .R< 0>
Created a new atom named: C36 within residue: .R< 0>
Created a new atom named: C15 within residue: .R< 0>
..................
FATAL: Atom .R< 0>.A<H3 70> does not have a type.
FATAL: Atom .R< 0>.A<C63 71> does not have a type.
FATAL: Atom .R< 0>.A<H6 72> does not have a type.
FATAL: Atom .R< 0>.A<C66 73> does not have a type.
FATAL: Atom .R< 0>.A<H2 74> does not have a type.
FATAL: Atom .R< 0>.A<C65 75> does not have a type.
FATAL: Atom .R< 0>.A<H1 76> does not have a type.
Failed to generate parameters
Parameter file was not saved.
Quit
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
- application/x-aportisdoc attachment: Test.pdb
Received on Tue Feb 07 2012 - 22:30:02 PST
