Hi, I tried the following two options, please suggest how to fix errors in
option2 if it is the correct way.
1) I removed the atoms causing the error from the PDB, and created bonds
connecting residues 417-418-419 (since 418 is CYP non-standard cysteine),
prmtop, inpcrd fails to generate.
2) If I don't create the bonds (I don't think this is correct), I get
following warnings about missing connections; prmtop, inpcrd generated.
Here tleap is ok with Fe-S bond. Can't understand why HEM is shown as ****?
Can you please suggest how to get parameters from newly generated bonds if
option 2 is not correct to use?
*Error with option 1*: prmtop inpcrd not generated
Warning: Close contact of 1.481424 angstroms between .R<LEU 451>.A<HD22 16>
and .R<PRO 461>.A<HG3 7>
Checking parameters for unit '1W0E'.
Checking for bond parameters.
Error: Could not find bond parameter for: C - N3
Checking for angle parameters.
Error: Could not find angle parameter: O - C - N3
Error: Could not find angle parameter: C - N3 - H
Error: Could not find angle parameter: C - N3 - H
Error: Could not find angle parameter: C - N3 - H
Error: Could not find angle parameter: C - N3 - CX
Error: Could not find angle parameter: CT - C - N3
Warning: There are missing parameters.
check: Warnings: 43
Unit is OK.
> saveamberparm 1W0E P450-1W0E-gas.prmtop P450-1W0E-gas.inpcrd
Checking Unit.
Warning: The unperturbed charge of the unit (3.000000) is not zero.
Note: Ignoring the warning from Unit Checking.
Building topology.
Building atom parameters.
Building bond parameters.
Error: Could not find bond parameter for: C - N3
Building angle parameters.
Error: Could not find angle parameter: O - C - N3
Error: Could not find angle parameter: C - N3 - H
Error: Could not find angle parameter: C - N3 - H
Error: Could not find angle parameter: C - N3 - H
Error: Could not find angle parameter: C - N3 - CX
Error: Could not find angle parameter: CT - C - N3
Building proper torsion parameters.
Error: ** No torsion terms for O-C-N3-H
Error: ** No torsion terms for O-C-N3-H
Error: ** No torsion terms for O-C-N3-H
Error: ** No torsion terms for O-C-N3-CX
Error: ** No torsion terms for CT-C-N3-H
Error: ** No torsion terms for CT-C-N3-H
Error: ** No torsion terms for CT-C-N3-H
Error: ** No torsion terms for CT-C-N3-CX
Building improper torsion parameters.
total 1485 improper torsions applied
Building H-Bond parameters.
Incorporating Non-Bonded adjustments.
Warning: Parameter file was not saved.
>
*Warnings with option 2:* prmtop, inpcrd generated
/opt/apps/apps/intel-17.0/amber/18-at19-may2019/bin/teLeap: Warning!
Close contact of 1.481424 angstroms between .R<LEU 451>.A<HD22 16> and
.R<PRO 461>.A<HG3 7>
Checking parameters for unit '1W0E'.
Checking for bond parameters.
Checking for angle parameters.
check: Warnings: 45
Unit is OK.
Total unperturbed charge: 3.000000
Total perturbed charge: 3.000000
Checking Unit.
/opt/apps/apps/intel-17.0/amber/18-at19-may2019/bin/teLeap: Warning!
The unperturbed charge of the unit (3.000000) is not zero.
/opt/apps/apps/intel-17.0/amber/18-at19-may2019/bin/teLeap: Note.
Ignoring the warning from Unit Checking.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
total 1482 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
**** 1
CASP 1
CYP 1
NGLY 1
NILE 1
)
(no restraints)
3 Cl- ions required to neutralize.
Adding 3 counter ions to "1W0E" using 1A grid
Grid extends from solute vdw + 2.51 to 8.51
Resolution: 1.00 Angstrom.
(no solvent present)
Calculating grid charges
Placed Cl- in 1W0E at (72.52, 77.71, -14.61).
Placed Cl- in 1W0E at (36.52, 87.71, 16.39).
Placed Cl- in 1W0E at (47.52, 106.71, 4.39).
Done adding ions.
Scaling up box by a factor of 1.337503 to meet diagonal cut criterion
Solute vdw bounding box: 48.016 76.349 66.864
Total bounding box for atom centers: 103.099 103.099 103.099
(box expansion for 'iso' is 51.9%)
Solvent unit box: 18.774 18.774 18.774
Volume: 564039.537 A^3 (oct)
Total mass 306874.188 amu, Density 0.903 g/cc
Added 13994 residues.
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
total 1482 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
* **** * 1
CASP 1
CYP 1
NGLY 1
NILE 1
WAT 13994
)
(no restraints)
On Wed, May 29, 2019 at 9:52 PM Vaibhav Dixit <vaibhavadixit.gmail.com>
wrote:
> Dear Prof. David Case and All,
> I am now getting a missing atomtype error shown below. One N-terminal
> residue and AS4 required by ConstpH simulations are causing fatal error. I
> was hoping these will be in covered with source leaprc.constph command.
> FYI, I solved the bond issue by (your suggestions) and saving new pdb in
> tleap, replacing *** with HEM, and reading it with new resids.
> I have bonded the CYP (CYS418 to 417 and 419) to using following bond
> commands, is this correct thing to do?
> Can you please suggest how to set the atomtype correctly for these (in the
> pdb or tleap or sourcing different forcefield)?
> thanks for your valuable suggestions.
>
> > savepdb 1W0E 1W0E-test.pdb
> Writing pdb file: 1W0E-test.pdb
>
> Warning: Truncating residue name for PDB format: **** -> ***
>
> Warning: Converting N-terminal residue name to PDB format: NGLY -> GLY
>
> Warning: Converting C-terminal residue name to PDB format: CASP -> ASP
> > 1W0E = loadpdb 1W0E-test.pdb
> Loading PDB file: ./1W0E-test.pdb
> +Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
> +---Tried to superimpose torsions for: *-NB-FE-*
> +--- With Sp2 - Sp0
> +--- Sp0 probably means a new atom type is involved
> +--- which needs to be added via addAtomTypes
> +Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
> +---Tried to superimpose torsions for: *-NA-FE-*
> +--- With Sp2 - Sp0
> +--- Sp0 probably means a new atom type is involved
> +--- which needs to be added via addAtomTypes
> +Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
> +---Tried to superimpose torsions for: *-ND-FE-*
> +--- With Sp2 - Sp0
> +--- Sp0 probably means a new atom type is involved
> +--- which needs to be added via addAtomTypes
> +Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
> +---Tried to superimpose torsions for: *-NC-FE-*
> +--- With Sp2 - Sp0
> +--- Sp0 probably means a new atom type is involved
> +--- which needs to be added via addAtomTypes
>
> *Created a new atom named: ND2 within residue: .R<AS4 417>Created a new
> atom named: H within residue: .R<NILE 419>*
> total atoms in file: 7761
> Leap added 3 missing atoms according to residue templates:
> 3 H / lone pairs
> *The file contained 2 atoms not in residue templates*
>
>
> *> bond 1W0E.1.FE 1W0E.418.SG <http://1W0E.418.SG>> bond 1W0E.417.C
> 1W0E.418.N> bond 1W0E.418.C 1W0E.419.N*
> > charge 1W0E
> Total unperturbed charge: 3.000000
> Total perturbed charge: 3.000000
> > addions 1W0E Cl- 0
> 3 Cl- ions required to neutralize.
> Adding 3 counter ions to "1W0E" using 1A grid
> Used default radius 1.50 for 2 atoms
> Grid extends from solute vdw + 2.51 to 8.51
> Resolution: 1.00 Angstrom.
> (no solvent present)
> Calculating grid charges
> Placed Cl- in 1W0E at (72.52, 77.71, -14.61).
> Placed Cl- in 1W0E at (36.52, 87.71, 16.39).
> Placed Cl- in 1W0E at (47.52, 106.71, 4.39).
>
> Done adding ions.
> > saveamberparm 1W0E P450-1W0E.prmtop P450-1W0E.rst7
> Checking Unit.
> FATAL: Atom .R<AS4 417>.A<ND2 21> does not have a type.
> FATAL: Atom .R<NILE 419>.A<H 22> does not have a type.
>
> Error: Failed to generate parameters
>
> Warning: Parameter file was not saved.
> > check 1W0E
> Checking '1W0E'....
> FATAL: Atom .R<AS4 417>.A<ND2 21> does not have a type.
> FATAL: Atom .R<NILE 419>.A<H 22> does not have a type.
>
> On Wed, May 29, 2019 at 5:04 PM David A Case <david.case.rutgers.edu>
> wrote:
>
>> On Wed, May 29, 2019, Vaibhav Dixit wrote:
>>
>> >I have tried setting the FE atom-type and bonding the Fe-S-Cys, but I'm
>> >unable to understand the correct syntax for specifying
>> atoms/residues/unit.
>>
>> >1W0E = loadpdb 1W0E_amber18.pdb
>> >bond 1W0E.A1501.43 1W0E.420.3408 #BOND CYS-S to HEM-FE
>>
>> Syntax is unit.residuenumber.atomname
>>
>> The residue number is the "Amber" residue number, starting at 1, and
>> incrementing by 1 for each new residue. For (perhaps not so good)
>> historical reasons, Amber has never made much use of chainId's, so
>> something like "A1501" won't be recognized. The atomname part would be
>> something like "FE" or "S".
>>
>> The tleap "charge" command gives the total charge on a unit: e.g.
>>
>> > charge GLU
>> Total unperturbed charge: -1.000000
>> Total perturbed charge: -1.000000
>>
>> I know it can be hard to find things in the manual. For tleap, I find the
>> interactive help environment to be the most useful. Typing "help" shows
>> you that there is a "charge" command, and typing "help charge" shows you
>> how to use it.
>>
>> ...hope this helps....dac
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
> --
>
> 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,
> ▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄
> 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
>
> P Please consider the environment before printing this e-mail
>
>
--
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,
▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄
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
P Please consider the environment before printing this e-mail
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Received on Thu May 30 2019 - 03:00:02 PDT
