Hi!
Sorry to be so long responding. Things got crazy for a while.
Did you get this worked out? If not, the problem is usually that you
need to tell leap to add a bond somewhere or you need to remove one or
more atoms, likely hydrogens.
Let me know if you still need help.
On Wed, Jun 12, 2019 at 10:12 AM Barb, Adam [BBMBS] <abarb.iastate.edu> wrote:
>
> Hello-
>
> I created an N-glycoprotein input file multiple ways: using the glycoprotein builder tool on the glycam website and manually preparing the files. Using either source of input file, I have the same problem: I have a non-integer charge when using GLYCAM_06EPb.
>
> This is what I input to tleap (Case A, no problem):
>
> source leaprc.protein.ff14SB
> source leaprc.GLYCAM_06j-1
> protein = loadpdb “test.pdb”
> check protein
>
> result: I have a charge of -8.000000
>
> Case B:
>
> source leaprc.protein.ff14SB
> source leaprc.GLYCAM_06j-1
> source leaprc.GLYCAM_06EPb
> protein = loadpdb “test.pdb”
> check protein
>
> result: I have a charge of -8.2430000
> I have run CheckMD on the output files and find that some carbohydrate residues (3xVMB, 3xVMA), have a charge of -0.1130 or 0.1130 (9x0MA) and -0.1940 (3xNLN). For Case A, all have charges of -0.1940 or 0.1940.
>
> Are there any suggestions for how I should modify my input pdb file to address the charge issue?
> (I have changed the N-glycosylated ASN residues to NLN, disulfide bonded CYS to CYX and added the specific bond in tleap as well as added N and C to the N and C term residues).
>
> Thank you!
>
> ADaM
>
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--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Wed Aug 21 2019 - 13:00:03 PDT
