Yes, I checked twice - it seems I provide correct filenames.
$ parmed.py 148l-du.prmtop
is the command, which produces the error.
Here is the complete bash script which reproduces the error.
#!/bin/bash
cat <<EOF > 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
EOF
cat <<EOF >DUM.frcmod
Parameters for DUmmy Atom
MASS
DU 100.0
NONBON 'RE'
DU 0.0 0.0
END
EOF
cat << EOF >test-du.pdb
REMARK default_name
ATOM 1 N MET 1 7.710 28.561 39.546 1.00 0.00 N
ATOM 2 CA MET 1 8.253 29.664 38.758 1.00 0.00 C
ATOM 3 HA MET 1 8.067 30.582 39.316 1.00 0.00 H
ATOM 4 CB MET 1 9.738 29.578 38.445 1.00 0.00 C
ATOM 5 HB2 MET 1 10.272 29.170 39.303 1.00 0.00 H
ATOM 6 HB3 MET 1 9.895 28.934 37.579 1.00 0.00 H
ATOM 7 CG MET 1 10.256 30.962 38.143 1.00 0.00 C
ATOM 8 HG2 MET 1 11.075 30.880 37.429 1.00 0.00 H
ATOM 9 HG3 MET 1 9.449 31.549 37.704 1.00 0.00 H
ATOM 10 SD MET 1 10.845 31.785 39.624 1.00 0.00 S
ATOM 11 CE MET 1 11.874 30.541 40.499 1.00 0.00 C
ATOM 12 HE1 MET 1 12.701 30.236 39.857 1.00 0.00 H
ATOM 13 HE2 MET 1 12.269 30.976 41.417 1.00 0.00 H
ATOM 14 HE3 MET 1 11.264 29.671 40.743 1.00 0.00 H
ATOM 15 C MET 1 7.445 30.133 37.548 1.00 0.00 C
ATOM 16 O MET 1 7.189 29.466 36.540 1.00 0.00 O
TER
ATOM 17 DU DU 2 30.120 30.394 45.942 1.00 0.00
TER
END
EOF
cat <<EOF >test.leap
source leaprc.ff14SB
loadamberparams DUM.frcmod
loadOff DUM.lib
m = loadpdb test-du.pdb
saveamberparm m test-du.prmtop test-du.inpcrd
quit
EOF
tleap -f test.leap
parmed.py test-du.prmtop
On 14 September 2015 at 18:04, Jason Swails <jason.swails.gmail.com> wrote:
>> Is it possible to load topology with pseudo atoms into Parmed?
>
>
> Yes, it should be fine. Are you sure you're not accidentally giving a
> coordinate file name as a prmtop, perhaps?
>
> What command and input are you using?
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Mon Sep 14 2015 - 09:30:11 PDT
