Dear Robert,
As Prof. Case said, a simple example would help a lot in debugging your issue.
However, you could already check a few things.
If you created new prep files, I assume that you build new residues.
If so, then you might want to be sure that your new residues have new residue names (meaning that they are not already defined in ff14SB).
You can use the "list" command in tleap to verify that, after "source leaprc.ff14SB".
By the way, if everything is fine after "loadamberprep unit_1.prepin", the residue name of your new residue should appear using the "list" command.
For example, let's say that you modified an alanine residue by changing one H of the methyl side chain with a Cl atom.
If you keep the residue name ALA, then leap could understand that it is a standard alanine residue, and then realize that one H is missing.
Leap would then simply add it and you would get one H and one Cl overlapping.
Then if your new units have new residue names, make sure that the atom/residue names in your "file_name.pdb" and "unit_[1-2].prepin" files do correspond.
The same issue as explained above would occur. But most probably, you would also get atom type definition errors as well.
Do the added atoms correspond to the atoms of your new residues ?
What happens if you try to save the parameters ? (saveamberparm)
Hope this helps.
Antoine
________________________________
-- Dr. Antoine MARION
Postdoctoral Research Scientist
Department of Life Sciences
Theoretical Chemical Biology and Protein Modelling Group
Technische Universität München
Emil-Erlenmeyer-Forum 8
D-85354 Freising-Weihenstephan
Germany
Phone: +49 (0)8161 71-2271
_______________________________________
From: David A Case <dacase.scarletmail.rutgers.edu>
Sent: Monday, October 12, 2015 2:45 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Prepgen difficulty
On Sun, Oct 11, 2015, Robert Molt wrote:
>
> source leaprc.ff14SB
> loadamberprep unit_1.prepin
> loadamberparams unit_1.frcmod
> loadamberprep unit_2.prepin
> loadamberparams unit_2.frcmod
> foo=loadpdb file_name.pdb
>
> for unit_1 and 2 are the new nucleic acid residues, file_name.pdb is the
> input geometry to which I would like to assign parameters. When I save a
> pdb to look at it, ....
I'm already lost: what commands did you use to "save a pdb"?
> the above description of overlapping atoms applies.
Also lost: can you be more explicit about what the "above description" means?
What evidence are you using to say that it "applies"?
> Moreover, in leap, when I load the pdb, there are many missing heavy
> atoms in the leap record for each of the new units. Hence why I have
> overlapping atoms.
A big problem with Amber documentation is the paucity of examples, but that
problem also applies here. How about providing an example? In my experience,
if I get a "missing heavy atom" message, it is usually straightforward to
compare the input pdb file with the prepin (or other library) file, and see
what is different. So you are going to have to provide a simple example to
help us see why you can't pinpoint the differences between the prepin and the
pdb files.
> 4.) This would lead me to believe that I must have a mistake in my .mc
> file listed above, that the connections are being made erroneously. I
> assume to just post that, although I can imagine someone asking for any
> of the other many commands involved in this complicated process (but for
> the sake of brevity, I will leave it as this, since short emails=good).
As in all debugging, try to make the "complicated process" simpler: do you
see the problem with just a single prepin file? Can you make a simple test
case for which you provide all the necessary files to reproduce it?
....dac
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Received on Mon Oct 12 2015 - 07:30:03 PDT
