Dear all,
I have experienced an issue with *pdb4amber* when dealing with SSBONDS
between chains, it renumbers the atoms after handling "TER", but it doesn't
update the CONECT record.
Thankfully, *Leap* produces a warning about this wrong connection.
The problem is restricted to AmberTools*17*, see bellow how to reproduce
for *1dwc.pdb*
# AmberTools 15
source /usr/local/amber14/amber.sh
pdb4amber -i 1dwc.pdb -o amber14.pdb
grep "ATOM 1196" amber14.pdb
ATOM 1196 SG CYX H 148 55.729 28.382 19.687 1.00 10.07
S
CONECT 24 1196
# AmberTools 17
source /usr/local/amber16/amber.sh
pdb4amber -i 1dwc.pdb -o amber16.pdb
grep "ATOM 1196" amber16.pdb
ATOM 1196 CB CYX H 148 55.173 26.880 20.510 1.00 10.00
C
CONECT 24 1196
--
Diego
--
Prof. Diego Enry B. Gomes, PhD
Laboratório de Biologia Computacional.
Diretoria de Metrologia Aplicada às Ciências da Vida.
Instituto Nacional de Metrologia, Qualidade e Tecnologia
+55 21 2145 3262 (3265, 3070, 3075) | dgomes.pq.cnpq.br
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Received on Mon Oct 30 2017 - 11:00:02 PDT
