Re: [AMBER] no bonds formed between AA and non-standard residue

From: Vaibhav Dixit <>
Date: Mon, 17 Feb 2020 18:41:12 +0900

Dear All.
As suggested by David, I tried parmed on prmtop/rst7 files.
It give 3 warnings for long bonds, one is between ILE420 and HEM which I
did connect using the bond commands shown at the bottom (leap.log
attached). But I can see these bonds in vmd, where I see terminal ProNH2
and ILECOO (as attached earlier).
Parmed doesn't mention residue number for 1st warnning for CYSs (I don't
think there is a disulfide bond in this protein, 3v8d). I wasn't expecting
the 3rd error as well, I had build 3 missing residue by overlapping/copying
these from 3sn5 for the same protein CYP7A1 (all other residues were
present, I'm hoping tleap will build any missing atoms for all of them give
backbone coords).

tleap log doesn't contain any errors after bond commands. It has some
warnings for missing improper torsions (it wrote the prmtop/rst7 files
anyway, should I be concerned about this?).
The result is the same even if I create a complex out of separate ligand
protein files or load a complexed pdb.
Please suggest further so that I can be sure that modified residue
(CYS-HEM) is connected to the main chain.

(base) [exx.c107739 xleap-mol2]$ parmed -p com.prmtop -c com.rst7

                                  /^^^/ /]
                                 / ] / ]
                         _______/ ]___ / ]
                        / \_____/ /
                      _/ [.] \ \ \
                     /.. | | ]
                      VVVvvv\ | | _/\ ]
          P A R M E D | / \ ]
                     AAA^^^^^ / \]
                      \_________\ \_____/
                                \ \

ParmEd: a Parameter file Editor

Loaded Amber topology file com.prmtop with coordinates from com.rst7

Reading input from STDIN...
> checkvalidity
Determining validity of prmtop
3 total warnings

MissingDisulfide: Detected two cysteine residues whose sulfur atoms are
within 3
                  Angstroms. Rename CYS to CYX in the PDB file and use the
                  'bond' command in tleap to create the disulfide bond

LongBondWarning: Atoms 6742 (ILE 420 [N]) and 7793 (HEM 482 [C3]) are
                 (equilibrium length 1.379 A) but are 4.898 A apart. This
                 indicates gaps in the original sequence and should be

LongBondWarning: Atoms 7256 (GLN 449 [C]) and 7258 (ALA 450 [N]) are bonded
                 (equilibrium length 1.335 A) but are 4.826 A apart. This
                 indicates gaps in the original sequence and should be


*tleap commands:*
source leaprc.protein.ff14SB
source leaprc.gaff
loadamberparams frcmod.ionsjc_tip3p
loadamberparams test-uncap1.frcmod
HEM = loadmol2 test-uncap3.mol2
3v8d = loadpdb 3v8d-prep.pdb
com = combine { 3v8d HEM }
bond com.482.C3 com.420.N
bond com.419.C com.482.N1
saveamberparm com com.prmtop com.rst7

On Mon, Feb 17, 2020 at 9:38 PM David A Case <> wrote:

> On Mon, Feb 17, 2020, Vaibhav Dixit wrote:
> >Even after combine option followed by bond commands, the expected bonds
> are
> >not generated as seen in vmd.
> First: use parmed to check for bonds: then it's easy to report exactly
> what you did to the list.
> Second: double check that there were no errors from tleap arising from
> the bond commands.
> Then: post as simple an example as you can, show exactly what bond
> command(s) you used in tleap, and what commands and results you got from
> parmed when you interrogated the resulting prmtop file.
> ....dac
> _______________________________________________
> AMBER mailing list

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,
P Please consider the environment before printing this e-mail

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Received on Mon Feb 17 2020 - 05:30:02 PST
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