I am working on a system that closely resembles this :
The oxygen is protonated so that there are three bonds involving oxygen.
I tried to create the prmtop and inpcrd files for this system using antechamber and xleap.
Using Antechamber, if I try to create to parameter files by using prepin file, I encounter lot of problems.
Initially I used a pdb file of the molecule generated using either vmd or molden. But antechamber finds error in running bondtype.
So, I shifted to gabedit to generate the structure and creating its pdb file. This works fine. Atleast antechamber does not get bondtype error here.
But, then, if you try to create prepin file using command:
$AMBERHOME/exe/antechamber -i F.pdb -fi pdb -o F.prepin -fo prepi -c bcc -s 2
you will face errors related to the charge on the system like:
INFO: Number of electrons is odd: 127
Please check the total charge (-nc flag) and spin multiplicity (-m flag)
As suggested you need to use -nc and -m flags to take care of charge and multiplicity of the system.
Once you take care of this error, your antechamber runs smoothly and generates corresponding prepin file.
We normally directly jump to parameter check.
If you try to do parameter check using command:
$AMBERHOME/exe/parmchk -i F.prepin -f prepi -o F.frcmod
You will most probably end up with segmentation fault error.
If we open prepin file, we might find some errors corresponding to the extra proton that is added on the oxygen.
35 O1 o M 33 32 30 1.254 121.207 -171.680 -0.227000
36 X 1 0 1 2.474 nan -9836.530 0.000000
Atom 36 is the one which corresponds to the extra H on oxygen. The bond type, bond distance, angle, dihedral data reported appears all wrong.
If you try to manually rectify this, you may succeed in generating the frcmod file.
But the catch here is if you visualize the molecule in xleap, you will find that the extra proton is not located on the oxygen as we expect, instead it is located on any neighboring carbon, nitrogen, oxygen(basically sp2 or sp moiety with probability to accept a proton).
After failing in many attempts to locate proton on desired oxygen, I took another approach. I tried to generate prmtop and inpcrd files using mol2 files instead of prepin.
Out of experience, working with prepin files is easier than mol2. But in this case mol2 worked well.
Using command:
antechamber -i F.pdb -fi pdb -o F.mol2 -fo mol2 -c bcc -s 2
along with -nc and -m flags for charge and multiplicity,
the mol2 file generated is more realistic. Parameters for all the atoms including the extra proton are well defined.
Parmchk also works fine and on viewing the molecule in xleap, the proton is located on desired oxygen.
The oxygen is protonated so that there are three bonds involving oxygen.
I tried to create the prmtop and inpcrd files for this system using antechamber and xleap.
Using Antechamber, if I try to create to parameter files by using prepin file, I encounter lot of problems.
Initially I used a pdb file of the molecule generated using either vmd or molden. But antechamber finds error in running bondtype.
So, I shifted to gabedit to generate the structure and creating its pdb file. This works fine. Atleast antechamber does not get bondtype error here.
But, then, if you try to create prepin file using command:
$AMBERHOME/exe/antechamber -i F.pdb -fi pdb -o F.prepin -fo prepi -c bcc -s 2
you will face errors related to the charge on the system like:
INFO: Number of electrons is odd: 127
Please check the total charge (-nc flag) and spin multiplicity (-m flag)
As suggested you need to use -nc and -m flags to take care of charge and multiplicity of the system.
Once you take care of this error, your antechamber runs smoothly and generates corresponding prepin file.
We normally directly jump to parameter check.
If you try to do parameter check using command:
$AMBERHOME/exe/parmchk -i F.prepin -f prepi -o F.frcmod
You will most probably end up with segmentation fault error.
If we open prepin file, we might find some errors corresponding to the extra proton that is added on the oxygen.
35 O1 o M 33 32 30 1.254 121.207 -171.680 -0.227000
36 X 1 0 1 2.474 nan -9836.530 0.000000
Atom 36 is the one which corresponds to the extra H on oxygen. The bond type, bond distance, angle, dihedral data reported appears all wrong.
If you try to manually rectify this, you may succeed in generating the frcmod file.
But the catch here is if you visualize the molecule in xleap, you will find that the extra proton is not located on the oxygen as we expect, instead it is located on any neighboring carbon, nitrogen, oxygen(basically sp2 or sp moiety with probability to accept a proton).
After failing in many attempts to locate proton on desired oxygen, I took another approach. I tried to generate prmtop and inpcrd files using mol2 files instead of prepin.
Out of experience, working with prepin files is easier than mol2. But in this case mol2 worked well.
Using command:
antechamber -i F.pdb -fi pdb -o F.mol2 -fo mol2 -c bcc -s 2
along with -nc and -m flags for charge and multiplicity,
the mol2 file generated is more realistic. Parameters for all the atoms including the extra proton are well defined.
Parmchk also works fine and on viewing the molecule in xleap, the proton is located on desired oxygen.
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