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
>
>
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>
--
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
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Received on Wed May 29 2019 - 14:00:02 PDT
