[AMBER] Antechamber on regular nucleotides

From: Mrinda Jones <mrindajones.gmail.com>
Date: Thu, 11 Jun 2015 18:28:14 +0530

I am trying to prepare prepin files for regular nucleotides (i.e. DA DT DG
DC) with the use of command:
antechamber -i DX.pdb -fi pdb -o DX.prepin -fo prepi -c bcc -j 4 -at amber
-nc -1

for DA, DG and DC, i am able to prepare prepin files but with DT I am
getting an error as
Warning: the assigned bond types may be wrong, please :
(1) double check the structure (the connectivity) and/or
(2) adjust atom valence penalty parameters in APS.DAT, and/or
(3) increase PSCUTOFF in define.h and recompile bondtype.c
    Be cautious, use a large value of PSCUTOFF (>100) will significantly
increase the computation time

Error: cannot run "/bin/bondtype -j full -i ANTECHAMBER_BOND_TYPE.AC0 -o
ANTECHAMBER_BOND_TYPE.AC -f ac" in judgebondtype() of antechamber.c
properly, exit

What is the origin of this error and how to rectify it?

I got required pdb files from tleap as :
>savepdb DA DA.pdb
>savepdb DT DT.pdb and so on...

why this error is happening with the pdb files prepared using amber residue

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Received on Thu Jun 11 2015 - 06:00:02 PDT
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