[AMBER] strange tleap error with bond command

From: Vaibhav Dixit <vaibhavadixit.gmail.com>
Date: Sat, 12 Jun 2021 11:31:45 +0530

Dear Amber users and developers,
I'm getting the following unexpected error with bond command.
The problem is with connecting residue 86 with residue 87 (named HD1).
The desc commands below shows that C and N of these residues are not
connected initially, thus I don't understand why I'm getting this error
trying to connect these residues.

The parmtop, inpcrd file get created if I avoid connecting 86 to 87, but
this leaves no bond between CO of 86 and NH of 87, which is not correct.
There are no connect records in the pdb as the error suggests.

Can you please help me troubleshoot this error?
Looking forward to valuable suggestions from the list.
I think I have made sure that this is not a silly mistake or a trivial
error with known solutions. thank you and best regards

Checking Unit.

Warning: The unperturbed charge of the unit (-0.999996) is not zero.

Note: Ignoring the warning from Unit Checking.

Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
!FATAL ERROR----------------------------------------
!FATAL: In file [unitio.c], line 1810
!FATAL: Message: 1-4: cannot add bond 3598 3600
This may be caused by duplicate bond specifications;
for example, explicit bond commands in addition to PDB conect records.

> desc mol.86.C
             Normal Perturbed
Name: C C
Type: C C
Charge: 0.5973 0.000
Polarization: 0.0000 0.000
Element: C (not affected by pert)
Atom flags: (decimal 131072 hex 0x20000)
        posfxd n posblt n posdrwn n selected n
        pert n notdisp n touched n posknwn Y
        internal n needsmin n needsbuild n
Atom position: 20.699000, 13.049000, 20.461000
Atom velocity: 0.000000, 0.000000, 0.000000
  Bonded to .R<LEU 86>.A<CA 3> by a single bond.
  Bonded to .R<LEU 86>.A<O 19> by a single bond.
> desc mol.87.N
Name: N
Type: N
Charge: -0.4157
Polarization: 0.0000
Element: N
Atom flags: (decimal 131072 hex 0x20000)
        posfxd n posblt n posdrwn n selected n
        pert n notdisp n touched n posknwn Y
        internal n needsmin n needsbuild n
Atom position: 20.049000, 12.406000, 19.505000
Atom velocity: 0.000000, 0.000000, 0.000000
  Bonded to .R<HD1 87>.A<H 2> by a single bond.
  Bonded to .R<HD1 87>.A<CA 3> by a single bond.

Dr. Vaibhav A. Dixit,
Visiting Scientist at the Manchester Institute of Biotechnology (MIB), The
University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
Assistant Professor,
Department of Pharmacy,
Birla Institute of Technology and Sciences Pilani (BITS-Pilani),
VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
Phone No. +91 1596 255652, Mob. No. +91-7709129400,
Email: vaibhav.dixit.pilani.bits-pilani.ac.in, vaibhavadixit.gmail.com
ORCID ID: https://orcid.org/0000-0003-4015-2941
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Received on Fri Jun 11 2021 - 23:30:04 PDT
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