AMBER Archive (2009)

Subject: [AMBER] atom type no recognize - xleap version 10 but fine in v 9

From: Peter Gannett (pgannett_at_hsc.wvu.edu)
Date: Fri Jun 19 2009 - 14:40:47 CDT

All:
 
I've an odd problem. I have been using the attached files for heme. By themselves or apart of P450s, they load fine and permit me to write out topology and coordinate files from xleap without complaint (ignoring a warning about a short bond and charge not being zero). I tried to use these for the same purpose with xleap in amber v10. I can not write topology/coordinate files and give me a message (see below) about the four heme nitrogens not being recognized (which does not happen in v9 or earlier). The specific error is about not being able to find an atom type which is defined in the frcmod file.
 
The install was recently performed (under linux), bugfixes for both ambertools and amber were downloaded/installed prior to compiling, all tests passed, and I've used it with both proteins and DNAs that required prep/frcmod files to be loaded for writing out topology/coordinate files without any difficulties. I spent a little time hunting for others who might have encountered such a problem but found none that specifically ID a situation where loading prep/frcmod files and writing out topology/coordinate files works for xleap with v9 but not v10.
 
Maybe I'm just missing something really simple.
 
Pete
 
Welcome to LEaP!
Sourcing leaprc: ./leaprc
Log file: ./leap.log
Loading parameters: /usr/local/amber10/dat/leap/parm/parm99.dat
Reading title:
PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP incl.02/04/99
Loading library: /usr/local/amber10/dat/leap/lib/all_nucleic94.lib
Loading library: /usr/local/amber10/dat/leap/lib/all_amino94.lib
Loading library: /usr/local/amber10/dat/leap/lib/all_aminoct94.lib
Loading library: /usr/local/amber10/dat/leap/lib/all_aminont94.lib
Loading library: /usr/local/amber10/dat/leap/lib/ions94.lib
Loading library: /usr/local/amber10/dat/leap/lib/solvents.lib
> loadamberprep hem_crg.prep
Loading Prep file: ./hem_crg.prep
> loadamberparams hem.frcmod
Loading parameters: ./hem.frcmod
Reading force field modification type file (frcmod)
Reading title:
remark goes here
> check HEM
Checking 'HEM'....
WARNING: The unperturbed charge of the unit: -0.999900 is not zero.
Warning: Close contact of 1.500285 angstroms between .R<HEM 1>.A<HBM 26> and .R<HEM 1>.A<HVC4 56>
Warning: Close contact of 1.500285 angstroms between .R<HEM 1>.A<HAM 32> and .R<HEM 1>.A<HVC2 46>
Checking parameters for unit 'HEM'.
Checking for bond parameters.
Checking for angle parameters.
check: Warnings: 3
Unit is OK.
> saveamberparm HEM xxx.top xxx.crd
Checking Unit.
WARNING: The unperturbed charge of the unit: -0.999900 is not zero.
 
 -- ignoring the warning.
 
Building topology.
Building atom parameters.
For atom: .R<HEM 1>.A<NA 2> Could not find type: NP
For atom: .R<HEM 1>.A<NB 48> Could not find type: NP
For atom: .R<HEM 1>.A<NC 58> Could not find type: NP
For atom: .R<HEM 1>.A<ND 72> Could not find type: NP
Parameter file was not saved.
 
 
 
 


  • application/octet-stream attachment: hem.prep


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