Can you send me test-du.prmtop and test-du.inpcrd so I can have a look at
them?
Thanks,
Jason
On Mon, Sep 14, 2015 at 12:23 PM, Mykola Dimura <dimura.mykola.gmail.com>
wrote:
> 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
>
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Sep 14 2015 - 10:00:04 PDT
