You need manually add a new line of "TER" under the line containing "OXT"
in your PDB file to separate the protein and ligand (or whatever after the
protein in PDB file) .
Junjun
On Tue, Feb 7, 2012 at 10:03 AM, Shuyi Cao <scao4.uic.edu> wrote:
> Hi all,
>
> I want to use MMPBSA to calculate binding energy formy protein conmplex,
> but my result is very weird, since the van der Waals energy is quite high.
> And an error message showed like this:
> INCONSISTENCIES EXIST WITHIN INTERNAL POTENTIAL TERMS (BOND, ANGLE, AND/OR
> DIHED).
> CHECK YOUR INPUT FILES AND SYSTEM SETUP. THESE RESULTS MAY NOT BE
> RELIABLE (check differences)!
> The most common cause of this is inconsistent charge definitions across
> topology files.
> Complex:
> Energy Component Average Std. Dev. Std. Err. of
> Mean
>
> -------------------------------------------------------------------------------
> BOND 7952096.0436 1239353.8273
> 177050.5468
> ANGLE 322047.5238 45147.3031
> 6449.6147
> DIHED 11885.5386 1351.0769
> 193.0110
> VDWAALS 255639253908530208.0000 1262730681757532416.0000
> 180390097393933216.0000
>
>
> Then I tried to use ante-MMPBSA to generate compatible files for MMPBSA.
> However, a error message showed like this:
> Warning: there is an atom OXT in residue ASP237 which does not exist in the
> model ASP!
> This atom will not be created.
> residue ASP237 has 13 atoms
> N
> H
> CA
> HA
> CB
> HB2
> HB3
> CG
> OD1
> OD2
> C
> O
> OXT
> model ASP has 12 atoms.
> N
> H
> CA
> HA
> CB
> HB2
> HB3
> CG
> OD1
> OD2
> C
> O
> Warning: cannot find template for residue ASP in our library.
> You will not be able to save prmtop for this molecule.
> But ASP 237 is actually the terminal residue of my protein, there must be
> an additional oxygen atom at the end of this residue. I did not quite get
> this error message. Could anyone help solve this problem?
>
> Thanks in advance for any help!
>
> --
> Shuyi Cao
> Graduate student
> Department of Medicinal chemistry and Pharmacognosy
> College of Pharmacy
> Univerisity of Illinois at Chicago
>
>
>
> --
> Shuyi Cao
> Graduate student
> Department of Medicinal chemistry and Pharmacognosy
> College of Pharmacy
> Univerisity of Illinois at Chicago
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Received on Mon Feb 06 2012 - 19:00:03 PST
