CCL: CHARMM: total charge not an integer
- From: "Venable, Richard (NIH/NHLBI) [E]" <venabler ~
nhlbi.nih.gov>
- Subject: CCL: CHARMM: total charge not an integer
- Date: Fri, 14 Aug 2009 12:10:37 -0400
Sent to CCL by: "Venable, Richard (NIH/NHLBI) [E]"
[venabler\a/nhlbi.nih.gov]
The forums at www.charmm.org can be quite helpful, esp. via the Search feature.
Molecules should have an integer charge; yours does not. Since chain terminal
patches NNUT and CNUT are not part of the standard distribution, you should
either look more closely at these two patch residues, or use more standard pairs
of end patches such as NTER/CTER (zwitterion) or ACE/CT3 (neutral, methyl).
--
Rick Venable 5635 FL/T906
Membrane Biophysics Section
NIH/NHLBI Lab. of Computational Biology
Bethesda, MD 20892-9314 U.S.A.
(301) 496-1905 venabler AT nhlbi*nih*gov
On 8/13/09 5:43 PM, "Natalia Zakharova nlzakh,,wsu.edu"
<owner-chemistry]~[ccl.net> wrote:
Sent to CCL by: "Natalia Zakharova" [nlzakh^_^wsu.edu]
I am currently trying to perform CHARMM (version c32b2) calculation for a
tri-peptide WGY (Trp-Gly-Tyr) with tryptophan side chain protonated at nitrogen.
When attmepting to run CHARMM, I get the following error:
***** Message from SEQRDR ***** THE SYSTEM CONTAINS 1 TITRATABLE GROUPS
THE USER MUST PREDETERMINE THE PROTONATION STATE THROUGH THE SEQUENCE AND RTF
HIS - 0 ASP - 0 GLU - 0 LYS - 0 TYR - 1
CHARMM> GENErate wgyneutral FIRST NNUT LAST CNUT SETup
THE PATCH 'NNUT' WILL BE USED FOR THE FIRST RESIDUE
THE PATCH 'CNUT' WILL BE USED FOR THE LAST RESIDUE
GENPSF> Segment 1 has been generated. Its identifier is WGYNEUTR.
Warning from PSFSUM: The sum of charges ( 1.090000) is not an integer
***** LEVEL 0 WARNING FROM <PSFSUM> *****
***** Total charge not an integer
I absolutely have no idea how to fix this issue and any help will be
appreciated.
Thank you,
Natalia Zakharova