Hello,
I parameterized boron and I created my *.frcmod file, for mol2 files,
everything was OK. I heated my molecule, calculated RMSD, minimized and
found very very close X-ray structure, I also calculated resp charges
exc.... exc... But yesterday I tried to run MMPSA for DNA-boron compund
complex.
Here is the things are getting worse:
1) I had to turn my bor.mol2 file to bor.pdb pdb file because I had to
use DNA.OL15 force filed too
so I went to this tutorial (SUSTIVA) :
http://ambermd.org/tutorials/basic/tutorial4b/index.html
and to use my gaff-compatible bor.frcmod file with bor.pdb instead of
bor.mol2 I run these commands (resp.mol2 is my boron mol2 file with resp
charges):
--------------------------------------------------------
source leaprc.gaff2
loadamberparams bor.frcmod
SUS =loadmol2 resp.mol2
saveoff SUS sus.lib
------------------------------------------------------------------
Then I converted my mol2 file into pdb file with antechamber
Then I changed "MOL2" residue to "SUS" residue
Then I opened tleap and here is I got warnings.... to much warnings..
------------------
tleap
-I: Adding /mnt/d/amber/amber16/dat/leap/prep to search path.
-I: Adding /mnt/d/amber/amber16/dat/leap/lib to search path.
-I: Adding /mnt/d/amber/amber16/dat/leap/parm to search path.
-I: Adding /mnt/d/amber/amber16/dat/leap/cmd to search path.
Welcome to LEaP!
(no leaprc in search path)
> source leaprc.gaff2
----- Source: /mnt/d/amber/amber16/dat/leap/cmd/leaprc.gaff2
----- Source of /mnt/d/amber/amber16/dat/leap/cmd/leaprc.gaff2 done
Log file: ./leap.log
Loading parameters: /mnt/d/amber/amber16/dat/leap/parm/gaff2.dat
Reading title:
AMBER General Force Field for organic molecules (Version 2.1, April 2016)
> loadamberparams bor.frcmod
Loading parameters: ./bor.frcmod
Reading force field modification type file (frcmod)
Reading title:
Remark line goes here
> loadoff sus.lib
Loading library: ./sus.lib
> p=loadpdb bor.
ERROR: syntax error
> a=loadpdb resp.pdb
Loading PDB file: ./resp.pdb
+Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
+---Tried to superimpose torsions for: *-O2-B1-*
+--- With Sp0 - 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: *-O1-B1-*
+--- With Sp0 - 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: *-C10-O2-*
+--- 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: *-C9-O1-*
+--- With Sp2 - Sp0
+--- Sp0 probably means a new atom type is involved
+--- which needs to be added via addAtomTypes
total atoms in file: 42
> check a
Checking 'a'....
Checking parameters for unit 'a'.
Checking for bond parameters.
Checking for angle parameters.
Unit is OK.
> saveamberparm a x.prmtop x.inpcrd
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
total 11 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
MOL 1
)
(no restraints)
> quit
----------------------------------------------
I ignored warnings to see what will happen and I went on simulation:
sander -O -i min.in -o min.out -p x.prmtop -c x.inpcrd -r min1.ncrst
I didn't get any error message but mdin file said:"nothing" :)
So I checked what happened and here is what I got :
ambpdb -p x.prmtop -c min1.ncrst > pdb.pdb
Error: Atom 31 was assigned a lower molecule # than previous atom.
Error: This can happen if bond information is incorrect or missing, or if
the
Error: atom numbering in molecules is not sequential. Try one of the
Error: following:
Error: - If this is a PDB file, try using the 'noconect' keyword.
Error: - If this topology did not have bond info, try increasing the bond
Error: search cutoff above 0.2 Ang. ('bondsearch <cutoff>').
Error: - Use the 'fixatomorder' command to reorder the topology and any
Error: associated coordinates.
Error: - Use the 'setMolecules' command in parmed to reorder only the
Error: topology.
Error: Could not determine molecule information for x.prmtop.
Error: SetSolventInfo: No molecule information.
Error: Could not determine solvent information for x.prmtop.
-------------
so here is my question:
How can I add boron atom into tleap? I also tried to add boron with
"addAtomTypes" command but it didn't work. tleap couldn't run impose
command (that's why when I use paramfit with boron I had to write my own
script to rotate dihedrals)
Thank you for your help by now
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Received on Sat Mar 14 2020 - 14:00:02 PDT
