Hi,
Your HOH residues are not recognised as 'water', because you haven't asked
HOH to be equivalent to the water model you intend to use.
E.g. for TIP3P, add this to tleap input before loading the pdb:
HOH = TP3
(It looks like you are using tleap from AmberTools16? Always good to
mention that...
If you are, you could use the 'old' cmd file that includes loading FF files
as well as setting HOH = TP3:
$AMBERHOME/dat/leap/cmd/oldff/leaprc.ff14SB )
HTH,
Marc
On 9 August 2016 at 15:20, Corum, Katharine W <katharine-corum.uiowa.edu>
wrote:
> 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
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Aug 09 2016 - 08:00:02 PDT
