AMBER Archive (2007)

Subject: AMBER: GDP UNKNOWN ATOM TYPE: O3 warning

From: j j (fantvamp_at_gmail.com)
Date: Sat Jul 21 2007 - 12:21:32 CDT

Dear amber users,
I´m thinking in use the GDP prepin and parm files from:
http://pharmacy.man.ac.uk/amber/
and I´ve downloaded both files:
GDP (revised phosphate parameters) PREP FRCMOD
When I load into leap these data, I got the following warnings
> GDP_dat = loadamberparams GDP.dat
Loading parameters: ./GDP.dat
(UNKNOWN ATOM TYPE: O3)
> loadAmberPrep GDP.prep
Loading Prep file: ./GDP.prep
(UNKNOWN ATOM TYPE: O3)
(UNKNOWN ATOM TYPE: O3)
(UNKNOWN ATOM TYPE: O3)
> GDP_loaded = loadpdb ./GDP.pdb
Loading PDB file: ./GDP.pdb
> saveamberparm GDP_loaded GDP_loaded.PARM GDP_loaded.INPCRD

I got both, the INPCRD and PARM, may this warning be put sideway?.

To avoid this, I though in join the GDP parms with another like maybe gaff.
I founded the parmjoin tool from:
http://amber.scripps.edu/antechamber/ac.html#parmjoin

11. parmjoin
Parmjoin combines a force field file and an additional force field file
(frcmod file)

Usage

Usage: parmjoin -p parm file -input
                -m frcmod file
                -o parm file - output

Example
parmjoin -p FFPARM.DAT -m frcmod -o newparm.dat

This command merge FFPARM.DAT and frcmod and generate a new force field file
- newparm.dat

but in the amber8 exe I´m using does not appear, so I downloaded the
antechamber package Version 1.27 ( antechamber-1.27.tar.gz ) from :
http://amber.scripps.edu/antechamber/download.html
After recompiling the parmjoin utility is not present,
config.h.old config.h
# This file sho # This file sho
# You will need # You will need
# installed. # installed.

SFX= SFX=
# uncomment the # uncomment the
#SFX=.exe #SFX=.exe

CC= gcc | CC= icc
CXX= g++ CXX= g++
CFLAGS= -O2 CFLAGS= -O2
OCFLAGS= -O3 OCFLAGS= -O3
FC= g77 | FC= ifort
FFLAGS = -O2 -f FFLAGS = -O2 -f
LEX= flex LEX= flex
RANLIB= ranlib RANLIB= ranlib
AR= ar rv AR= ar rv
LM= -lm LM= -lm

Files attached:
GDP.prep
GDP.dat
GDP.pdb
load_4GDP.leap
leap.log
leap_GDP.log
GDP_loaded.PARM
GDP_loaded.INPCRD
imake.log
make.log
Thank you,
JJ




  • chemical/x-pdb attachment: GDP.pdb


  • application/octet-stream attachment: leap.log




  • application/octet-stream attachment: imake.log

  • application/octet-stream attachment: make.log
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