Dear David and AMBER users,
thank you for the advice, but this doesn't seem to work for AmberTools15.
(Currentl I use Amber14 and AmberTools 15)
I renamed the atoms at OHE residues.
MODEL 1
HETATM 1 OP3 OHE A 1 -2.273 -8.313 -1.809 1.00 0.00
O
HETATM 2 HOP3 OHE A 1 -2.030 -8.446 -0.861 1.00 0.00
H
HETATM 3 P DT A 2 -0.819 -8.604 -2.581 1.00 0.00
P
...and so on
And then... it didn't recognize the atoms at OHE
nikolay/amber14# tleap
-I: Adding /home/nikolay/amber14/dat/leap/prep to search path.
-I: Adding /home/nikolay/amber14/dat/leap/lib to search path.
-I: Adding /home/nikolay/amber14/dat/leap/parm to search path.
-I: Adding /home/nikolay/amber14/dat/leap/cmd to search path.
Welcome to LEaP!
Sourcing leaprc: /home/nikolay/amber14/dat/leap/cmd/leaprc
Log file: ./leap.log
Loading parameters: /home/nikolay/amber14/dat/leap/parm/parm10.dat
Reading title:
PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA
Loading parameters: /home/nikolay/amber14/dat/leap/parm/frcmod.ff14SB
Reading force field modification type file (frcmod)
Reading title:
ff14SB protein backbone and sidechain parameters
Loading library: /home/nikolay/amber14/dat/leap/lib/amino12.lib
Loading library: /home/nikolay/amber14/dat/leap/lib/aminoct12.lib
Loading library: /home/nikolay/amber14/dat/leap/lib/aminont12.lib
Loading library: /home/nikolay/amber14/dat/leap/lib/nucleic12.lib
Loading library: /home/nikolay/amber14/dat/leap/lib/atomic_ions.lib
Loading library: /home/nikolay/amber14/dat/leap/lib/solvents.lib
> dna1=loadpdb serg32_BDNA_5p_OHE_david.pdb
Loading PDB file: ./serg32_BDNA_5p_OHE_david.pdb
Created a new atom named: OP3 within residue: .R<OHE 1>
Created a new atom named: HOP3 within residue: .R<OHE 1>
Added missing heavy atom: .R<OHE 1>.A<O 2>
Created a new atom named: OP3 within residue: .R<OHE 34>
Created a new atom named: HOP3 within residue: .R<OHE 34>
Added missing heavy atom: .R<OHE 34>.A<O 2>
total atoms in file: 2034
Leap added 4 missing atoms according to residue templates:
2 Heavy
2 H / lone pairs
The file contained 4 atoms not in residue templates
Since added/missing = extra, there is a high probability
of atoms with 'incorrect' names; you may want to
use addPdbAtomMap to map these names, or change in file
>
What would be a solution for AmberTools15/Amber14 then?
P.S. Can AmberTools 17 be used together with Amber14?
I do have plans to acquire Amber18 which will be released in a couple of
months
(am I right?) so it hardly makes sense to buy Amber16 now.
Kind regards,
Nick
Message: 6
Date: Wed, 21 Feb 2018 07:48:24 -0500
From: David A Case <david.case.rutgers.edu>
Subject: Re: [AMBER] "The unperturbed charge of the unit is not
integral": really nothing to care about?
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
<20180221124824.bmfq57iuxipphdq7.vpn-client-172-16-8-64.rutgers.edu>
Content-Type: text/plain; charset=us-ascii
On Wed, Feb 21, 2018, Nikolay N. Kuzmich wrote:
>
> The DNA molecule has the phosphate groups on its 5' ends.
> And I suspect that non-integral charge originates from that.
> The OHE residue was created accordingly.
> This is how one 5'-end looks like:
You don't say what version of Amber you are using, or what commands you
gave to tleap. But the following works for me:
1. Change the atom names in the OHE residue in the pdb file to OP3 and
HOP3,
to match the PDB standard.
2. source both leaprc.RNA.OL3 and leaprc.DNA.OL5 (or bsc1). (The OHE
residue is only in the RNA library; cc-ing to Tom Cheatham for advice
on what the best thing to do here is.
3. load the pdb file into tleap and call saveAmberParm. This gives
a charge of -1.0002, which is close enough to -1 for government work.
Note that you will need AmberTools17.
...good luck....dac
Dear David and AMBER users,
The DNA molecule has the phosphate groups on its 5' ends.
And I suspect that non-integral charge originates from that.
The OHE residue was created accordingly.
This is how one 5'-end looks like:
MODEL 1
HETATM 1 O OHE A 1 -2.273 -8.313 -1.809 1.00 0.00
O
HETATM 2 H OHE A 1 -2.030 -8.446 -0.861 1.00 0.00
H
HETATM 3 P DT A 2 -0.819 -8.604 -2.581 1.00 0.00
P
HETATM 4 OP1 DT A 2 -0.816 -7.797 -4.046 1.00 0.00
O1-
HETATM 5 OP2 DT A 2 -0.618 -10.237 -2.827 1.00 0.00
O
HETATM 6 O5' DT A 2 0.423 -8.007 -1.635 1.00 0.00
O
HETATM 7 C5' DT A 2 1.429 -7.769 -2.593 1.00 0.00
C
HETATM 8 C4' DT A 2 2.670 -7.211 -1.915 1.00 0.00
C
HETATM 9 O4' DT A 2 2.538 -5.761 -1.810 1.00 0.00
O
HETATM 10 C1' DT A 2 2.250 -5.395 -0.468 1.00 0.00
C
HETATM 11 N1 DT A 2 1.010 -4.500 -0.436 1.00 0.00
N
HETATM 12 C6 DT A 2 -0.268 -4.992 -0.479 1.00 0.00
C
HETATM 13 C5 DT A 2 -1.329 -4.177 -0.394 1.00 0.00
C
HETATM 14 C7 DT A 2 -2.732 -4.706 -0.440 1.00 0.00
C
HETATM 15 C4 DT A 2 -1.157 -2.754 -0.255 1.00 0.00
C
HETATM 16 O4 DT A 2 -2.068 -1.932 -0.171 1.00 0.00
O
HETATM 17 N3 DT A 2 0.161 -2.348 -0.221 1.00 0.00
N
HETATM 18 C2 DT A 2 1.273 -3.161 -0.306 1.00 0.00
C
HETATM 19 O2 DT A 2 2.405 -2.707 -0.266 1.00 0.00
O
HETATM 20 C3' DT A 2 2.911 -7.677 -0.478 1.00 0.00
C
HETATM 21 C2' DT A 2 2.089 -6.682 0.343 1.00 0.00
C
HETATM 22 O3' DT A 2 4.249 -7.615 -0.007 1.00 0.00
O
HETATM 23 H5' DT A 2 1.069 -7.051 -3.329 1.00 0.00
H
HETATM 24 H5'' DT A 2 1.684 -8.704 -3.092 1.00 0.00
H
HETATM 25 H4' DT A 2 3.535 -7.360 -2.561 1.00 0.00
H
HETATM 26 H1' DT A 2 3.036 -4.739 -0.093 1.00 0.00
H
HETATM 27 H6 DT A 2 -0.435 -6.057 -0.538 1.00 0.00
H
HETATM 28 H71 DT A 2 -2.887 -5.399 0.387 1.00 0.00
H
HETATM 29 H72 DT A 2 -3.436 -3.878 -0.356 1.00 0.00
H
HETATM 30 H73 DT A 2 -2.894 -5.226 -1.384 1.00 0.00
H
HETATM 31 H3 DT A 2 0.343 -1.278 -0.117 1.00 0.00
H
HETATM 32 H3' DT A 2 2.503 -8.680 -0.348 1.00 0.00
H
HETATM 33 H2' DT A 2 1.332 -7.219 0.915 1.00 0.00
H
HETATM 34 H2'' DT A 2 2.746 -6.144 1.027 1.00 0.00
H
With O instead of -O1 for the OP1 atom the result was the same.
This DNA double-helix was created using NAB,
then the phosphate groups were added manually via Schrodinger Maestro,
then I renamed DT5 to DT and created OHE residue, some atoms were
re-grouped and renamed
and the resulted PDB was passed through the pdb4amber.
The 3' ends have not been changed after NAB and remained as by default.
Thank you in advance,
Nick
On Mon, Feb 19, 2018, Nikolay N. Kuzmich wrote:
>
> when checking the charge of a DNA model tleap reports error that the
> unperturbed charge
> of the unit is -64.172.
We would need to know details of how you constructed the DNA model: if you
have 5' and 3' units on the ends, the charge should be integral (and equal
to
the number of phosphate groups.) You are right to be concerned, but
resolution depends on exactly what you did.
....dac
Dear AMBER users and developers,
when checking the charge of a DNA model tleap reports error that the
unperturbed charge
of the unit is -64.172. I performed the google search on the topic and
found out that it is just a warning. But from another hand that means it is
impossible to fully neutralize the system
and the residul charge may lead to unrealistic behaviour.
The AmberTools15 is used.
What should be done in this situation?
Sincerely,
Nick
Nikolay Kuzmich
Department of Drug Safety,
Research Institute of Influenza,
WHO National Influenza Centre of Russia,
15/17 Professor Popov St.,
Saint-Petersburg
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Received on Thu Feb 22 2018 - 08:30:02 PST
