Dear AMBER community,
I have a problem loading an Amber topology file which contains
custom-made dummy atoms into parmed.py. I'm using dummy atoms to
indirectly pull on the groups of atoms, connecting the dummy atom to
the molecule with NMR restraints.
So I created frcmod and lib files (see below) and use them to make
topologies with leap. Obtained topologies work well with pmemd.
However, when I try to load such a topology with Parmed.py, I get an
error:
#####
ParmEd: a Parameter file Editor
Traceback (most recent call last):
File "/home/user/opt/amber14/bin/parmed.py", line 126, in <module>
amber_prmtop.add_parm(parm)
File "/home/user/opt/amber14/lib/python2.7/site-packages/ParmedTools/parmlist.py",
line 38, in add_parm
raise ParmError('Added parm must be Structure or a subclass')
ParmedTools.exceptions.ParmError: Added parm must be Structure or a subclass
#####
Is it possible to load topology with pseudo atoms into Parmed?
#load.leap:
source leaprc.ff14SB
loadamberparams DUM.frcmod
loadOff DUM.lib
m = loadpdb mol_DU.pdb
saveamberparm m mol-du.prmtop mol-du.inpcrd
#mol_DU.pdb:
...
TER
ATOM 1234 DU DU 123 0.000 0.000 0.000 1.00 0.00 ??
TER
...
#DUM.frcmod:
Parameters for DUmmy Atom
MASS
DU 100.0
NONBON 'RE'
DU 0.0 0.0
END
#DUM.lib:
!!index array str
"DU"
!entry.DU.unit.atoms table str name str type int typex int resx
int flags int seq int elmnt dbl chg
"DU" "DU" 0 1 131072 1 0 0.000000
!entry.DU.unit.atomspertinfo table str pname str ptype int ptypex
int pelmnt dbl pchg
"DU" "DU" 0 -1 0.0
!entry.DU.unit.boundbox array dbl
-1.000000
0.0
0.0
0.0
0.0
!entry.DU.unit.childsequence single int
2
!entry.DU.unit.connect array int
0
0
!entry.DU.unit.hierarchy table str abovetype int abovex str
belowtype int belowx
"U" 0 "R" 1
"R" 1 "A" 1
!entry.DU.unit.name single str
""
!entry.DU.unit.positions table dbl x dbl y dbl z
0.0 0.0 0.0
!entry.DU.unit.residueconnect table int c1x int c2x int c3x int
c4x int c5x int c6x
0 0 0 0 0 0
!entry.DU.unit.residues table str name int seq int childseq int
startatomx str restype int imagingx
"DU" 1 2 1 "?" 0
!entry.DU.unit.residuesPdbSequenceNumber array int
1
!entry.DU.unit.solventcap array dbl
-1.000000
0.0
0.0
0.0
0.0
!entry.DU.unit.velocities table dbl x dbl y dbl z
0.0 0.0 0.0
Best regards, Mykola Dimura.
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Received on Mon Sep 14 2015 - 09:00:02 PDT
