Dear Samuel,
Thanks for your answer. My previous problem (cannot run
"/share/apps/amber/amber14/bin/sqm
-O -i sqm.in -o sqm.out" of bcc() in charge.c properly, exit) was solved.
Now, I have another problem. For my protein structure, I used following
commands:
$AMBERHOME/exe/reduce pr_h.pdb > pr.pdb
tleap -f pr.in
pr.in file is as follows:
source leaprc.ff99SB
pr = loadpdb pr.pdb
set default PBRadii mbondi2
saveamberparm pr pr.prmtop pr.inpcrd
quit
---------------------------------------------------------
But, I encountered with:
FATAL: Atom .R<CLEU 124>.A<H04 25> does not have a type.
FATAL: Atom .R<CLEU 124>.A<H05 26> does not have a type.
FATAL: Atom .R<CLEU 124>.A<H06 27> does not have a type.
FATAL: Atom .R<CLEU 124>.A<H07 28> does not have a type.
FATAL: Atom .R<CLEU 124>.A<H08 29> does not have a type.
FATAL: Atom .R<CLEU 124>.A<H09 30> does not have a type.
FATAL: Atom .R<CLEU 124>.A<H10 31> does not have a type.
FATAL: Atom .R<CLEU 124>.A<H11 32> does not have a type.
FATAL: Atom .R<CLEU 124>.A<H12 33> does not have a type.
FATAL: Atom .R<CLEU 124>.A<H13 34> does not have a type.
Failed to generate parameters
Parameter file was not saved.
There is this error for most of the Hydrogen atoms.
How to resolve this problem?
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Sep 13 2016 - 23:00:02 PDT
