[AMBER] Non-integer charge problem with tleap using GLYCAM_06EPb but not GLYCAM_06j-1

From: Barb, Adam [BBMBS] <abarb.iastate.edu>
Date: Wed, 12 Jun 2019 14:12:03 +0000

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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Received on Wed Jun 12 2019 - 07:30:04 PDT
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