Hi,
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
library?
Regards,
M.Jones
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jun 11 2015 - 06:00:02 PDT
