Re: [AMBER] Non-standard KCX residue with missing hydrogen on carbamate and charge -1

From: David A Case via AMBER <>
Date: Thu, 5 Jan 2023 09:28:38 -0500

On Thu, Jan 05, 2023, Barbara Herlah via AMBER wrote:
>I have a question regarding preparation of a non-standard KCX residue that has a charge -1.
>> antechamber -i el_grid.out -fi gout -bk KCX -fo ac -o -c bcc -at amber -nc -1 -m 1 -rn KCX

At this point, check the charges in the file: do they look
reasonable? Do they sum to -1? Things are probably fine, but a double-check
won't hurt.

>I also checked the NEWPDB.PDB file and it looks good - like a KCX residue
>should. There are two double bonds between C and O atoms missing in this
>representation however.

Looking at a PDB file is not a good way to find bonds, since that
information is not present in the file. The visualization program is just
guessing, using heuristics.

>/apps/amber/amber20/bin/teLeap: Warning!
>addIons: 1st Ion & target unit have charges of the same sign:
> unit charge = -2e-06; ion1 charge = -1;
> can't neutralize.

Do you expect the charge in your input pdb file (which created unit "a") to
have a net charge of zero. If so, you can't use zero in the addIons command
to neutralize the system. You need to explicitly say how many sodium and
chloride ions you want to add.

>/apps/amber/amber20/bin/teLeap: Warning!
>There is a bond of 8.716 angstroms between O3 and C2 atoms:
>------- .R<KCX 198>.A<O3 22> and .R<KCX 198>.A<C2 23>
>/apps/amber/amber20/bin/teLeap: Warning!
>There is a bond of 3.202 angstroms between O1 and C4 atoms:
>------- .R<KCX 198>.A<O1 5> and .R<KCX 198>.A<C4 6>

These are things you can check: does your input pdb file not have good bonds
here? You could still try some minimization to see if things improve.

>When I look the .pdb created by the, it doesn0t look like the KCX
>residue is connected to the protein since we can see the dotted line where
>a residue should be in a cartoon vizualization.

Again, don't use visualization of a pdb file here. Use the printBonds
action in parmed to check to see what bonds are actually in the prmtop file.

>When I vizualize the first .nc file created it somehow forms wierd bonds
>and connects the residue in a loop.

See above about using parmed to look at the connectivity you have.
>2. Regarding the lack of bond created
>Should I have written in file for the bond to be created?
>bond a./number_of_residue1/.C a./number_of_residue2/.N
>bond a./number_of_residue2/.N a./number_of_residue3/.C

If a bond is missing, the above will be needed.

...hope this helps....dac

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Received on Thu Jan 05 2023 - 06:30:03 PST
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