Dear Bongkeun,
Usually rounding off errors are between +/-.0001 and +/-.0006.
"The unperturbed charge: 0.01" means there is something wrong in the
charge derivation procedure for your molecule. If this is a whole
molecule and not a molecular fragment this is even more surprising...
This is difficult to help as you did not describe how you derived the
charges for your SAM structure.
regards, Francois
Quoting Bongkeun Kim <bkim.chem.ucsb.edu>:
> 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 - 08:00:06 PDT
