Hi Prof Case...and Jason,
Many Thanx for the speedy reply.
>[In general, careful editing of the input pdb file is required for all but the
>simplest protein or nucleic acid systems, and a careful review of what you are
>loading is always desirable.]
Indeed so, I agree!
>Then load your force field and any libraries needed for the GDP or Mg
>moieties. Issue a single loadpdb command to create the basic system,
>follow this by bond, solvateBox and addIons, etc. as appropriate. Then
>examine the prmtop file that is created to make sure you have the residues
>and ions you want.
This is what I have *intended* to do, but obviously, not *exactly* what I did. :) The tutorials are very good for the beginner, where a standard protocol is identified (which is what you mention above). This is what I did, although there were a system-specific tweaks, as always. Additionally, I use xleap to prep the inpcrd/prmtop files and always use the 'check' command before creating these files - in your opinion, would you expect xleap 'check' to pick up such errors?
FYI, I created this prmtop, using the method you specify above (and that which is detailed in the tutorial). The only difference here is that I implement PM3 qm for the GDP/Mg. ESP charges are calculated in gaussian and then the RESP program is used in AMBER. The pdb file is then edited to contain the calculated charges, with a few minor changes (to make the system neutral) and resulting lib file is saved. The fact that the prmtop *thinks* there are two GDP in the residue labels but only one in the ATOMS_PER_MOLECULE confuses me. Can anything RE the source of the problem be taken from this specific info, or is it simply...the topology file is wrong and needs fixed?
Finally, the fact that residue labels seems to think there are 2 GDP molecules - is this likely the source of the PMEMD error...I don't know anything about intermolecular PRFs, but think I read that this could be due to overlapping atoms. Is this true?
Many Thanx for the advice.
Maura
---------------------------------------------------------------
Maura Mooney
School of Chemistry and Chemical Engineering
David Keir Building
Queens University Belfast
Stranmillis Road
Belfast
BT9 5AG
mmooney05.qub.ac.uk
mauramooney9.gmail.com
________________________________________
From: David A Case [case.biomaps.rutgers.edu]
Sent: 16 June 2011 15:13
To: AMBER Mailing List
Subject: Re: [AMBER] PMEMD does not support intermolecular PRFs
On Thu, Jun 16, 2011, Maura Catherine Mooney wrote:
>
> I have little/no experience reading topology files, but I had a look,
> based on your response. Strange behaviour indeed, as there is only
> *intended* to be one GDP molecule, one Mg and 4 coordinating H2O's.
You need to review how you created the topology file in the first place.
I recommend creating a single PDB file with exactly what you want in
it. Change any H2O or HOH labels to WAT; put a TER card between separate
molecules. Remove CONECT records (but be sure to issue a "bond" command
later to leap for any disulfide bonds or other non-standard bonds.) It is
best to put all the water molecules at the end. If there are alternate
conformations in file, choose the one(s) you want and remove the rest.
[In general, careful editing of the input pdb file is required for all but the
simplest protein or nucleic acid systems, and a careful review of what you are
loading is always desirable.]
Then load your force field and any libraries needed for the GDP or Mg
moieties. Issue a single loadpdb command to create the basic system,
follow this by bond, solvateBox and addIons, etc. as appropriate. Then
examine the prmtop file that is created to make sure you have the residues
and ions you want.
...good luck.....dac
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Received on Thu Jun 16 2011 - 08:00:04 PDT
