I have been trying to intercalate a drug into a 6 base pair sequence of DNA
and covalently attach the drug. I am able to convert the drug pdb file to
prepin, then add the drug to a piece of DNA generated by nucgen, intercalate
the drug into the binding site and save the prmtop and inpcrd files in
Amber8. Then attach the drug covalently (in xleap) i save the file as pdb
then use antechamber to generate charges to create a prepin file so i can
generate the correct files for molecular modeling. But so far i an unable
to create the prepin file.
To get around this i tried importing a mol2 (fin.mol2) file from InsightII
and convert it to prepin. When i run the command: antechamber -i fin.mol2
-fi mol2 -o fin.prepin -o prepi -c gas
And i get the following.
The atom number exceeds the MAXATOM, reallocate memory
Cannot successfully assign bond type for this molecule, please :
(1) double check the structure (the connectivity) and/or
(2) adjust atom valence penalty parameters in APS.DAT, and/or
(3) increase MAXVASTATE in define.h and recompile bondtype.C
No Gasteiger parameter for atom[30]:P :p, exit(0)
So i tried a different charge method: antechamber -i fin.mol2 -fi mol2 -o
fin.prepin -o prepi -c bcc
And this is printed out.
The atom number exceeds the MAXATOM, reallocate memory
Cannot successfully assign bond type for this molecule, please :
(1) double check the structure (the connectivity) and/or
(2) adjust atom valence penalty parameters in APS.DAT, and/or
(3)increase MAXVASTATE in define.h and recompile bondtype.C
The molecule contains 463 atoms (MAXATOM set to 2000, MAXVASTATE 5000). The
mol2 file has been successfully opened in rasmol, insighII and macspartin
with no problem. I have attaches a copy of the mol2 file (fin.mol2) and
hope that you can give me insight into how to create the prepin file so a
can load the molecule into xleap and save the prmtop and inpcrd files.
Thanks in advance.
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- application/octet-stream attachment: fin.mol2
Received on Fri May 27 2005 - 01:53:01 PDT
