Hi, Thanks for the responses. Here are the steps I have used to try and create .prmtop and .inpcrd files for a protein that will hopefully contain 2 water molecules.
1. I first used a protein crystal structure and deleted all but 2 water oxygen atoms (I can get the .prmtop and .inpcrd files when I start with no water oxygen atoms)
2. I added H atoms to the structure by using the command: $AMBERHOME/bin/pdb4amber -i original.pdb -o new.pdb --reduce
H atoms are added to the protein but not the water O atoms. My water section in the pdb remains:
HETATM 619 O HOH 47 1.172 37.091 64.942
HETATM 620 O HOH 48 -1.649 31.925 65.942
3. Next I use tleap: $AMBERHOME/bin/tleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.protein.ff14SB
4. I next load the new.pdb file: protein = loadpdb new.pdb and I get this message:
Loading PDB file: ./new.pdb
Unknown residue: HOH number: 46 type: Terminal/beginning
..relaxing end constraints to try for a dbase match
-no luck
Unknown residue: HOH number: 47 type: Terminal/last
..relaxing end constraints to try for a dbase match
-no luck
Creating new UNIT for residue: HOH sequence: 47
Created a new atom named: O within residue: .R<HOH 47>
Creating new UNIT for residue: HOH sequence: 48
Created a new atom named: O within residue: .R<HOH 48>
total atoms in file: 620
Leap added 24 missing atoms according to residue templates:
24 H / lone pairs
The file contained 2 atoms not in residue templates
5. Then when I try to create the .prmtop and .inpcrd files by using the command saveamberparm protein protein.prmtop protein.inpcrd I get this message:
Checking Unit.
FATAL: Atom .R<HOH 47>.A<O 1> does not have a type.
FATAL: Atom .R<HOH 48>.A<O 1> does not have a type.
Failed to generate parameters
Parameter file was not saved.
The program obviously can tell that these two oxygen atoms will belong to water because it says HOH but I can't get the H atoms added to these oxygen atoms.
Thanks!
Katie
________________________________
From: David A Case <david.case.rutgers.edu>
Sent: Tuesday, August 9, 2016 6:52:06 AM
To: AMBER Mailing List
Subject: Re: [AMBER] Setting up a pdb file for a QM/MM calculation with explicit water
On Mon, Aug 08, 2016, Corum, Katharine W wrote:
> My water molecule oxygen atoms do not get H atoms placed on them. I
> can use another program to add H but when I use tleap to generate the
> name.prmtop and name.inpcrd files I run into issues when explicit water
> molecules are present.
Just saying that you "ran into issues" is not very informative. LEaP
generally has no problem in adding hydrogens to water molecules. There must
be something special about your case that is inhibiting this. But without
knowing exactly what you did, and (more imprortantly) anything about what
problems you might have encountered, people on the list will not be able to
provide much help.
...dac
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Received on Tue Aug 09 2016 - 07:30:03 PDT
