Hello,
I made a kind of the SAM structure with S((CH2)n-CH3)2 monomer.
I was able to generate residue topology file from this monomer as a
name of "LIC". "LIC_bcc.prepi" file was used to load into tleap. And I
wanted to load a pdb file which has about more than 10 LIC residues.
This is all the input/output:
-------------------------------------------------------
tleap -f leaprc.ff99SB
> source leaprc.gaff
> loadamberprep LIC_bcc.prepi
Loading Prep file: ./LIC_bcc.prepi
> sam6=loadpdb samch3r9.pdb
Loading PDB file: ./samch3r9.pdb
total atoms in file: 621
> check sam6
Checking 'sam6'....
Checking parameters for unit 'sam6'.
Checking for bond parameters.
Checking for angle parameters.
Unit is OK.
> sam7=loadpdb samch3r10.pdb
Loading PDB file: ./samch3r10.pdb
total atoms in file: 690
> check sam7
Checking 'sam7'....
ERROR: The unperturbed charge of the unit: 0.010000 is not integral.
WARNING: The unperturbed charge of the unit: 0.010000 is not zero.
Checking parameters for unit 'sam7'.
Checking for bond parameters.
Checking for angle parameters.
check: Errors: 1 Warnings: 1
> quit
-------------------------------------------------------
In sum up, loading of 9 LIC molecules has no problem, but if I load
more than 10 molecules from pdb files, I always get 0.001 times the
number of monomers(the upper case, 0.001*10= 0.01 is not integral).
I just want to know what causes this error.
I attached all the files for you to look at, prepi file, monomer pdb
file, 9-mer pdb file and 10-mer pdb file.
Bongkeun Kim
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Received on Fri Sep 24 2010 - 00:00:05 PDT
