Dear all,
I'm parameterizing a small organic molecule(named cie.mol2, the structure is attached) using "bcc" charge method in Amber9, the command was as follows:
antechamber -fi mol2 -fo prepi -i cie.mol2 -o cie.prepi -c bcc -at gaff -j 4 -rn CIE -s 2
when this command was executed, following messages came out one by one:
Running: /home/yuzhih/apps/antechamber127/exe/bondtype -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac -j full
Running: /home/yuzhih/apps/antechamber127/exe/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff
Total number of electrons: 214; net charge: 0
Running: $AMBERHOME/exe/divcon
Error: cannot run "$AMBERHOME/exe/divcon" of bcc() in charge.c properly, exit
from the attached "divcon.out" file, I found out that the problem of "NO CONVERGENCE IN SCF CALCULATION" was still existed even if I had increased the MAXIT from default of 100 to 5000, while when the same command was executed in Amber8, everything went on wheels, the resulted divcon.out file was also attached named as "divcon_use_amber8.out".
well, my questions are:
1. excpet change the conformation of cie.mol2(because I want to keep the initial conformation just as it was in the pdb file of a complex system), how can I resolve the problem of "NO CONVERGENCE IN SCF CALCULATION" in divcon? I think that it's not very efficient just increasing the MAXIT?
2. for the same cie.mol2 and the same command, the divcon program in Amber8 went on wheels while the one in Amber9 crashed, moreover, in my result of "make test.serial" in Amber9, a test related to divcon (/home/yuzhih/apps/amber9/test/qmmm2/crambin) didn't passed just because of the problem of "NO CONVERGENCE IN SCF CALCULATION". Then is there something wrong with my program of divcon in Amber9? what can I do to compile a correct divcon in Amber9?
any advices will be greatly appreciated, thanks in advance!
yours sincerely, Zhihong Yu
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- application/octet-stream attachment: cie.mol2
Received on Sun Sep 17 2006 - 06:07:04 PDT
