[AMBER] FATAL atom does not have a type crispr cas9 pdb

From: Jisha B <jisha.b.k0511.gmail.com>
Date: Sun, 30 Aug 2020 09:07:47 +0530

Dear all,
I have been trying to generate a topology and parameter file for a CRISPR
cas9 system. I have done the
pdb4amber -i cas1.pdb -o cas.pdb --reduce --dry
In tleap
source leaprc.protein.ff14SB
source leaprc.RNA.OL3
source leaprc.DNA.bsc1
source leaprc.water.tip3p
system = loadpdb cas.pdb
addions system Na+ 0
solvatebox system TIP3PBOX 12.0
saveamberparm system cas.prmtop cas.inpcrd

But I get the following error.
FATAL: Atom .R<DA5 1523>.A<P 31> does not have a type. FATAL: Atom .R<DA5
1523>.A<OP1 32> does not have a type. FATAL: Atom .R<DA5 1523>.A<OP2 33>
does not have a type.
How to solve this problem? Kindly advise 

-- 
Jisha
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Aug 29 2020 - 21:00:02 PDT
Custom Search