Hey,
I have downloaded a pdb file from www.rcsb.org, as shown in the attachment
(1X6W.pdb).
It cannot be regonized by Amber force fields directly because there is a
TMS residue that is not included in any force field. So I use antechamber to
generate a new pdb file and run it in Gaff. It goes like follows:
$AMBERHOME/exe/antechamber -i 1X6W_3.pdb -fi pdb -o newff.pdb -fo pdb
And 1X6W_3.pdb is revised pdb file for antechamber. There are error
messages like the following:
Unrecognized atomic name JB, exit
Unrecognized atomic name JB, exit
Unrecognized atomic name JA, exit
For atom[28]:E2, the best APS is not zero, bonds involved by this atom are
frozen
For atom[29]:GA, the best APS is not zero, bonds involved by this atom are
frozen
For atom[30]:GB, the best APS is not zero, bonds involved by this atom are
frozen
For atom[31]:GC, the best APS is not zero, bonds involved by this atom are
frozen
For atom[32]:A1TT, the best APS is not zero, bonds involved by this atom are
frozen
For atom[33]:B1TT, the best APS is not zero, bonds involved by this atom are
frozen
For atom[38]:E3, the best APS is not zero, bonds involved by this atom are
frozen
For atom[41]:B6, the best APS is not zero, bonds involved by this atom are
frozen
For atom[42]:B7, the best APS is not zero, bonds involved by this atom are
frozen
For atom[46]:JB, the best APS is not zero, bonds involved by this atom are
frozen
For atom[47]:JA, the best APS is not zero, bonds involved by this atom are
frozen
For atom[48]:KA, the best APS is not zero, bonds involved by this atom are
frozen
For atom[49]:KB, the best APS is not zero, bonds involved by this atom are
frozen
For atom[50]:LB, the best APS is not zero, bonds involved by this atom are
frozen
For atom[51]:LA, the best APS is not zero, bonds involved by this atom are
frozen
---Judge bond type for Residue 1 with ID of 1 and Name of S ---
The frozen atom type can only be 1, 2, 3, 7 (aromatic single), 8 (aromatic
double)Error: cannot run
"/itc/apps/amber/10/amber10/bin/bin.Linux.x86_64/bondtype -j full -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac" in
judgebondtype() of antechamber.c properly, exit
What is that problem? It really puzzles me!
Thank you very much!
Best,
Yikan
Received on Wed Sep 02 2009 - 23:05:23 PDT
