Dear All (and David),
I removed the TER card between residues 420 and 421, then used bond command
as shown below.
This has bonded the non-std residue CYS-HEM with main chain as expected.
tleap adds amide bond between 420 and 421, which I want to delete using
parmed deletebond command.
I tried giving atom number and residue numbers, but both the commands show
error. It wrote the new prmtop/rst7 files anyways, but vmd is unable to
open these files. ambpdb generated pdb with conect shows all the bonds
including extra-ones. Not sure what's happening here.
Can you please suggest how to selectively delete the long-bond between
420-421 and any other extra bonds I don't want? (I'm assuming that it will
also delete parameter information associated with that bond)
Thank you very much for your help and valuable advice.
(base) [exx.c107739 xleap-mol2]$ tleap
-I: Adding /usr/local/amber18/dat/leap/prep to search path.
-I: Adding /usr/local/amber18/dat/leap/lib to search path.
-I: Adding /usr/local/amber18/dat/leap/parm to search path.
-I: Adding /usr/local/amber18/dat/leap/cmd to search path.
Welcome to LEaP!
(no leaprc in search path)
> source leaprc.protein.ff14SB
----- Source: /usr/local/amber18/dat/leap/cmd/leaprc.protein.ff14SB
----- Source of /usr/local/amber18/dat/leap/cmd/leaprc.protein.ff14SB done
Log file: ./leap.log
Loading parameters: /usr/local/amber18/dat/leap/parm/parm10.dat
Reading title:
PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA
Loading parameters: /usr/local/amber18/dat/leap/parm/frcmod.ff14SB
Reading force field modification type file (frcmod)
Reading title:
ff14SB protein backbone and sidechain parameters
Loading library: /usr/local/amber18/dat/leap/lib/amino12.lib
Loading library: /usr/local/amber18/dat/leap/lib/aminoct12.lib
Loading library: /usr/local/amber18/dat/leap/lib/aminont12.lib
> source leaprc.gaff
----- Source: /usr/local/amber18/dat/leap/cmd/leaprc.gaff
----- Source of /usr/local/amber18/dat/leap/cmd/leaprc.gaff done
Log file: ./leap.log
Loading parameters: /usr/local/amber18/dat/leap/parm/gaff.dat
Reading title:
AMBER General Force Field for organic molecules (Version 1.81, May 2017)
> loadamberparams frcmod.ionsjc_tip3p
Loading parameters: /usr/local/amber18/dat/leap/parm/frcmod.ionsjc_tip3p
Reading force field modification type file (frcmod)
Reading title:
Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham
JPCB (2008)
> loadamberparams test-uncap1.frcmod
Loading parameters: ./test-uncap1.frcmod
Reading force field modification type file (frcmod)
Reading title:
Remark line goes here
> HEM = loadmol2 test-uncap3.mol2
Loading Mol2 file: ./test-uncap3.mol2
Reading MOLECULE named HEM
> 3v8d = loadpdb 3v8d-prep.pdb
Loading PDB file: ./3v8d-prep.pdb
Added missing heavy atom: .R<NSER 1>.A<OG 10>
Added missing heavy atom: .R<ARG 3>.A<CG 8>
Added missing heavy atom: .R<ARG 3>.A<CD 11>
Added missing heavy atom: .R<ARG 3>.A<NE 14>
Added missing heavy atom: .R<ARG 3>.A<CZ 16>
Added missing heavy atom: .R<ARG 3>.A<NH1 17>
Added missing heavy atom: .R<ARG 3>.A<NH2 20>
Added missing heavy atom: .R<ASN 13>.A<CG 8>
Added missing heavy atom: .R<ASN 13>.A<OD1 9>
Added missing heavy atom: .R<ASN 13>.A<ND2 10>
Added missing heavy atom: .R<LYS 39>.A<CE 14>
Added missing heavy atom: .R<LYS 39>.A<NZ 17>
Added missing heavy atom: .R<LYS 64>.A<NZ 17>
Added missing heavy atom: .R<LYS 70>.A<CG 8>
Added missing heavy atom: .R<LYS 70>.A<CD 11>
Added missing heavy atom: .R<LYS 70>.A<CE 14>
Added missing heavy atom: .R<LYS 70>.A<NZ 17>
Added missing heavy atom: .R<MET 94>.A<CG 8>
Added missing heavy atom: .R<MET 94>.A<SD 11>
Added missing heavy atom: .R<MET 94>.A<CE 12>
Added missing heavy atom: .R<LYS 108>.A<CD 11>
Added missing heavy atom: .R<LYS 108>.A<CE 14>
Added missing heavy atom: .R<LYS 108>.A<NZ 17>
Added missing heavy atom: .R<GLU 120>.A<CD 11>
Added missing heavy atom: .R<GLU 120>.A<OE1 12>
Added missing heavy atom: .R<GLU 120>.A<OE2 13>
Added missing heavy atom: .R<SER 135>.A<OG 8>
Added missing heavy atom: .R<LYS 139>.A<CG 8>
Added missing heavy atom: .R<LYS 139>.A<CD 11>
Added missing heavy atom: .R<LYS 139>.A<CE 14>
Added missing heavy atom: .R<LYS 139>.A<NZ 17>
Added missing heavy atom: .R<LYS 176>.A<CD 11>
Added missing heavy atom: .R<LYS 176>.A<CE 14>
Added missing heavy atom: .R<LYS 176>.A<NZ 17>
Added missing heavy atom: .R<ARG 206>.A<NE 14>
Added missing heavy atom: .R<ARG 206>.A<CZ 16>
Added missing heavy atom: .R<ARG 206>.A<NH1 17>
Added missing heavy atom: .R<ARG 206>.A<NH2 20>
Added missing heavy atom: .R<GLU 222>.A<CG 8>
Added missing heavy atom: .R<GLU 222>.A<CD 11>
Added missing heavy atom: .R<GLU 222>.A<OE1 12>
Added missing heavy atom: .R<GLU 222>.A<OE2 13>
Added missing heavy atom: .R<LYS 226>.A<CE 14>
Added missing heavy atom: .R<LYS 226>.A<NZ 17>
Added missing heavy atom: .R<GLU 283>.A<CD 11>
Added missing heavy atom: .R<GLU 283>.A<OE1 12>
Added missing heavy atom: .R<GLU 283>.A<OE2 13>
Added missing heavy atom: .R<LYS 286>.A<CE 14>
Added missing heavy atom: .R<LYS 286>.A<NZ 17>
Added missing heavy atom: .R<LYS 302>.A<CG 8>
Added missing heavy atom: .R<LYS 302>.A<CD 11>
Added missing heavy atom: .R<LYS 302>.A<CE 14>
Added missing heavy atom: .R<LYS 302>.A<NZ 17>
Added missing heavy atom: .R<GLU 306>.A<CG 8>
Added missing heavy atom: .R<GLU 306>.A<CD 11>
Added missing heavy atom: .R<GLU 306>.A<OE1 12>
Added missing heavy atom: .R<GLU 306>.A<OE2 13>
Added missing heavy atom: .R<ASN 308>.A<CG 8>
Added missing heavy atom: .R<ASN 308>.A<OD1 9>
Added missing heavy atom: .R<ASN 308>.A<ND2 10>
Added missing heavy atom: .R<GLU 392>.A<CG 8>
Added missing heavy atom: .R<GLU 392>.A<CD 11>
Added missing heavy atom: .R<GLU 392>.A<OE1 12>
Added missing heavy atom: .R<GLU 392>.A<OE2 13>
Added missing heavy atom: .R<LYS 395>.A<CG 8>
Added missing heavy atom: .R<LYS 395>.A<CD 11>
Added missing heavy atom: .R<LYS 395>.A<CE 14>
Added missing heavy atom: .R<LYS 395>.A<NZ 17>
Added missing heavy atom: .R<GLU 442>.A<OE1 12>
Added missing heavy atom: .R<GLU 442>.A<OE2 13>
Added missing heavy atom: .R<LYS 451>.A<CG 8>
Added missing heavy atom: .R<LYS 451>.A<CD 11>
Added missing heavy atom: .R<LYS 451>.A<CE 14>
Added missing heavy atom: .R<LYS 451>.A<NZ 17>
Added missing heavy atom: .R<CHIE 481>.A<OXT 18>
Added missing heavy atom: .R<CHIE 481>.A<CG 8>
Added missing heavy atom: .R<CHIE 481>.A<ND1 9>
Added missing heavy atom: .R<CHIE 481>.A<CD2 14>
Added missing heavy atom: .R<CHIE 481>.A<CE1 10>
Added missing heavy atom: .R<CHIE 481>.A<NE2 12>
total atoms in file: 3813
Leap added 3962 missing atoms according to residue templates:
80 Heavy
3882 H / lone pairs
> com = combine { 3v8d HEM }
> bond com.482.C3 com.421.N
> bond com.420.C com.482.N1
> saveamberparm com com2.prmtop com2.rst7
Checking Unit.
Warning: There is a bond of 4.825647 angstroms between:
Warning: There is a bond of 3.680325 angstroms between:
Warning: The unperturbed charge of the unit (3.077800) is not integral.
Warning: The unperturbed charge of the unit (3.077800) is not zero.
Note: Ignoring the error and warnings from Unit Checking.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
total 1615 improper torsions applied
Building H-Bond parameters.
Incorporating Non-Bonded adjustments.
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
(Residues lacking connect0/connect1 -
these don't have chain types marked:
res total affected
CHIE 1
HEM 1
NSER 1
)
(no restraints)
> quit
Quit
Exiting LEaP: Errors = 0; Warnings = 4; Notes = 1.
(base) [exx.c107739 xleap-mol2]$ parmed -p com2.prmtop -c com2.rst7
./ | | \.
.:( |i __ j| ):`.
.' `._ |`::::'| _.' `.
.' "---.j `::' f.---" `.
_____/ ___ ____ __ __ ____ ___
| \ | | | `__'| \ / || | | \
| .-. | .' `| | .-. |-/| \/ || ___| | . \
| |_| | | i | | |_| /"":| || | | | \ \
| / | .^. | | /::::| || |__. | | \ \
| ----' | | | | | \ :: | || __| | | | )
| | .' ''' `.| |\ \ | i i j| | . | / /
| | | _ || | \ \ | |\/| || |__. | |. / .
[| | | | | || | \ \ | | | || | | / ].
] `--' :--' `--::--' \_|`--' ::--"|____|-"-- / :[
| __ ::-'''`.:' "--. .----::.----:: ,.---._ :|
[ .-"" "`' \ / " `' `-. :].
]:.' \/ `.:[
|/ \|
ParmEd: a Parameter file Editor
Loaded Amber topology file com2.prmtop with coordinates from com2.rst7
Reading input from STDIN...
> checkvalidity
Determining validity of prmtop
2 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 7253 (GLN 449 [C]) and 7255 (ALA 450 [N]) are bonded
(equilibrium length 1.335 A) but are 4.826 A apart. This
often
indicates gaps in the original sequence and should be
checked
carefully.
> printbonds :420,421
Atom 1 Atom 2 R eq Frc Cnst Distance
Energy
6761 N ( N) 7790 C3 ( c) 1.3790 427.6000 1.3105
2.0071
6762 CD ( CT) 6761 N ( N) 1.4490 337.0000 1.4814
0.3547
6765 CG ( CT) 6762 CD ( CT) 1.5260 310.0000 1.4985
0.2338
6768 CB ( CT) 6765 CG ( CT) 1.5260 310.0000 1.4941
0.3149
6771 CA ( CX) 6761 N ( N) 1.4490 337.0000 1.4745
0.2185
6771 CA ( CX) 6768 CB ( CT) 1.5260 310.0000 1.5218
0.0055
6773 C ( C) 6771 CA ( CX) 1.5220 317.0000 1.5324
0.0346
6773 C ( C) 6775 N ( N) 1.3350 490.0000 1.3384
0.0057
6774 O ( O) 6773 C ( C) 1.2290 570.0000 1.2361
0.0290
6744 CA ( CX) 6742 N ( N) 1.4490 337.0000 1.4869
0.4839
6746 CB ( 3C) 6744 CA ( CX) 1.5260 310.0000 1.5402
0.0624
6748 CG2 ( CT) 6746 CB ( 3C) 1.5260 310.0000 1.5186
0.0169
6752 CG1 ( 2C) 6746 CB ( 3C) 1.5260 310.0000 1.5371
0.0382
6755 CD1 ( CT) 6752 CG1 ( 2C) 1.5260 310.0000 1.5089
0.0907
6759 C ( C) 6744 CA ( CX) 1.5220 317.0000 1.5399
0.1016
* 6759 C ( C) 6761 N ( N) 1.3350 490.0000 3.6803
2695.2695*
6759 C ( C) 7783 N1 ( n) 1.3790 427.6000 0.7438
172.5172
6760 O ( O) 6759 C ( C) 1.2290 570.0000 1.2231
0.0198
6740 C ( C) 6742 N ( N) 1.3350 490.0000 1.3349
0.0000
6763 HD2 ( H1) 6762 CD ( CT) 1.0900 340.0000 1.0900
0.0000
6764 HD3 ( H1) 6762 CD ( CT) 1.0900 340.0000 1.0900
0.0000
6766 HG2 ( HC) 6765 CG ( CT) 1.0900 340.0000 1.0900
0.0000
6767 HG3 ( HC) 6765 CG ( CT) 1.0900 340.0000 1.0900
0.0000
6769 HB2 ( HC) 6768 CB ( CT) 1.0900 340.0000 1.0900
0.0000
6770 HB3 ( HC) 6768 CB ( CT) 1.0900 340.0000 1.0900
0.0000
6772 HA ( H1) 6771 CA ( CX) 1.0900 340.0000 1.0900
0.0000
6743 H ( H) 6742 N ( N) 1.0100 434.0000 1.0100
0.0000
6745 HA ( H1) 6744 CA ( CX) 1.0900 340.0000 1.0900
0.0000
6747 HB ( HC) 6746 CB ( 3C) 1.0900 340.0000 1.0900
0.0000
6749 HG21 ( HC) 6748 CG2 ( CT) 1.0900 340.0000 1.0900
0.0000
6750 HG22 ( HC) 6748 CG2 ( CT) 1.0900 340.0000 1.0900
0.0000
6751 HG23 ( HC) 6748 CG2 ( CT) 1.0900 340.0000 1.0900
0.0000
6753 HG12 ( HC) 6752 CG1 ( 2C) 1.0900 340.0000 1.0900
0.0000
6754 HG13 ( HC) 6752 CG1 ( 2C) 1.0900 340.0000 1.0900
0.0000
6756 HD11 ( HC) 6755 CD1 ( CT) 1.0900 340.0000 1.0900
0.0000
6757 HD12 ( HC) 6755 CD1 ( CT) 1.0900 340.0000 1.0900
0.0000
6758 HD13 ( HC) 6755 CD1 ( CT) 1.0900 340.0000 1.0900
0.0000
> deleteBond :420,421
Bad command deleteBond:
deleteBond <mask1> <mask2>
> deleteBond 420 421
Bad command deleteBond:
deleteBond <mask1> <mask2>
> deleteBond 420 421 verbose
Bad command deleteBond:
deleteBond <mask1> <mask2>
> deletebond :420,421
Bad command deleteBond:
deleteBond <mask1> <mask2>
> deletebond 6759 6761
Bad command deleteBond:
deleteBond <mask1> <mask2>
> outparm com2-1.prmtop com2-1.rst7
Outputting Amber topology file com2-1.prmtop and restart com2-1.rst7
Action outparm failed
FileExists: com2-1.prmtop exists; not overwriting.
> outparm com2-1.prmtop com2-1.rst7
Outputting Amber topology file com2-1.prmtop and restart com2-1.rst7
> outpdb com2-1.pdb
Writing PDB file com2-1.pdb renumbering atoms and residues
>
On Tue, Feb 18, 2020 at 10:28 PM David A Case <david.case.rutgers.edu>
wrote:
> On Tue, Feb 18, 2020, Vaibhav Dixit wrote:
>
> >I think tleap residues start with 0, but in the pdb/prmtop-rst7 it writes
> >first residue as 1.
>
> After you load you pdb, you can use the "desc" command in tleap to see
> what the residue identies and numbers are. You should find that leap
> starts numbering residues at 1.
>
> >But strangely, the terminal OXT atom is still present, do I need to
> >explicitly delete it? Should it not get deleted when I bond the residue to
> >another standard/non-standard ones?
>
> It's still not clear exactly what you are doing. Is the OXT atom in the
> input PDB file? If so, you need to get rid of it, assuming that it is
> not at the C-terminus of a protein chain.
> >
> >I think the fact that terminal OXT and NH atoms for 420, 421 are still
> >there is a problem and needs fixing before regular MD (min, heat, equil)
> >jobs can be started.
>
> I agree. My suggestion: make a single PDB file that has just the atoms
> that should be there. Make sure that the TER cards are in the
> appropriate places. Then, if tleap tries to add an unwanted atom back
> in, you will know that the libraries you are loading don't match the PDB
> file you have (and which has the atoms you want.)
>
> ....dac
>
>
--
Regards,
Dr. Vaibhav A. Dixit,
Visiting Scientist at the Manchester Institute of Biotechnology (MIB), The
University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
AND
Assistant Professor,
Department of Pharmacy,
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Birla Institute of Technology and Sciences Pilani (BITS-Pilani),
VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
India.
Phone No. +91 1596 255652, Mob. No. +91-7709129400,
Email: vaibhav.dixit.pilani.bits-pilani.ac.in, vaibhavadixit.gmail.com
http://www.bits-pilani.ac.in/pilani/vaibhavdixit/profile
https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/
ORCID ID: https://orcid.org/0000-0003-4015-2941
http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
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Received on Tue Feb 18 2020 - 22:00:02 PST
