Hi Hashem,
Thanks for your suggestions, there was some progress when I copied the
standard residues. But now I'm getting following error:
### ### ### ###
### MTK++ Info ###
### Function: stdFrag::generateCoordinates ###
### Message:
ATOM 1 HH31 XXX A 1A 1.392 1.956 -0.000
ATOM 2 CH3 XXX A 1A 0.808 2.876 0.000
ATOM 3 HH32 XXX A 1A 0.180 2.908 0.890
ATOM 4 HH33 XXX A 1A 0.180 2.908 -0.890
ATOM 5 C XXX A 1A 1.718 4.106 -0.000
ATOM 6 O XXX A 1A 2.941 3.977 -0.000
### ### ### ###
### ### ### ###
### MTK++ Error ###
### Function: protonate::buildMissingHeavyAtoms ###
### Message:
New atom on top of atom 4884
### ### ### ###
### ### ### ###
### MTK++ Error ###
### Function: protonate::runMol ###
### Message: Residue AC1:1 contains 3 heavy atoms, should contain 6
### ### ### ###
-----------------------------------------
Similarly for NE1, the error is
### ### ### ###
### MTK++ Error ###
### Function: protonate::runMol ###
### Message: Residue NE1:3 contains 2 heavy atoms, should contain 6
### ### ### ###
-----------------------------------------
Could you please suggest how to debug these errors.
Thanks again,
Manish
-----Original Message-----
From: Hashem Taha [mailto:htahaphd.gmail.com]
Sent: Tuesday, May 03, 2011 3:05 PM
To: AMBER Mailing List
Subject: Re: [AMBER] MCPB problem
I'm not sure if this is the cause of your errors, but there may be a
problem with the residue names that you are using to create your model
(e.g. AC1 or NE1 and others). All the residue names should be defined in
the libraries that you load in (i.e. NAME_params.xml, NAME.xml, and all
standard libraries).
I think that when you use "createResidue AC1 in CLR" for example, the
residue AC1 is unrecognized and therefore producing an error. You should
either use "ACE" (and "NME" instead of NE1) or use the following command
to copy the standard residues to AC1 or NE1.
copyStdResidue aminoAcids94/ACE NAME/AC1
copyStdResidue aminoAcids94/NME NAME/NE1
Let me know if this helps,
Hashem
On 5/3/11 12:31 PM, "Manish" <manish.datt.hotmail.com> wrote:
>Hi All,
>
>
>
>I'm trying to MCPB to calculate parameters for tetrahedrally coordinated
>Zinc ion in a protein following the MTK++ manual. The first part with the
>sidechain runs fine. But with the large part the calculations are getting
>stuck. These have been running for 60 hours. Is it expected? Tail of the
>log
>file is below:
>
>### ### ### ###
>
>### MTK++ Info ###
>
>### Function: watProtonate::setup ###
>
>### Message:
>
>Number of sphere grid points = 1098
>
>Allocating sphereGridCoords: 3294 ints
>
>Allocating maxPairs: 1098 ints
>
>Allocating Hs: 106506 ints
>
>Allocating lonePairs: 213012 ints
>
>### ### ### ###
>
>
>
>### ### ### ###
>
>### MTK++ Info ###
>
>### Function: protonate::runMol ###
>
>### Message: CLR
>
>### ### ### ###
>
>--------------------------------------------------------------------------
>--
>----
>
>
>
>Attached is the complete log file. Please suggest if should try something
>else or just run longer.
>
>
>
>Thanks,
>
>
>
>Manish
>
>
>
>
>
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Received on Tue May 03 2011 - 14:30:02 PDT
