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"FIRST NTER LAST CT3" does NOT work!
#3723 10/14/04 12:57 AM
Joined: Apr 2004
Posts: 5
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jana Offline OP
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Hi!
I was trying to build a single peptide with "First NTER LAST CT3". Below is the error message which does not make sense since NH3 and HA are not even bonded.

What seems to be strange is that "FIRST ACE LAST CT3", "FIRST NTER LAST CTER" and other combinations that have both termini charged or uncharged work just fine. Maybe I am missing somthing here? Any insight would be appreciated!

- Jana



CHARMM> generate @name2 FIRSt NTER LAST CT3 SETUp
Parameter: NAME2 -> "MODL"
THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE
THE PATCH 'CT3' WILL BE USED FOR THE LAST RESIDUE
: No angle parameters for 1 ( HA NH3 HA )
: No angle parameters for 2 ( HA NH3 HA )
: No angle parameters for 3 ( HA NH3 CT1 )
: No angle parameters for 4 ( HA NH3 HA )
: No angle parameters for 5 ( HA NH3 CT1 )
: No angle parameters for 6 ( HA NH3 CT1 )
: No angle parameters for 7 ( NH3 HA CT3 )
: No angle parameters for 8 ( NH3 HA CT3 )
: No angle parameters for 9 ( NH3 HA CT3 )
: A TOTAL OF 9 MISSING PARAMETERS

The input file:
* build ntlys
* test

! set some aliases
!-----------------
set name = ntlys
set resname = lys
set step = 1
set topfile = top_all22_prot_cmap.inp
set parfile = par_all22_prot_cmap.inp

! fast version of charmm
! ----------------------
faster on

! Read topology and parameter files
! ---------------------------------
open unit 1 read form name @topfile
read rtf card unit 1
close unit 1

open unit 1 read form name @parfile
read param card unit 1
close unit 1

set name2 = MODL

! Read sequence
! -------------
read sequence card
1
@resname

WRNlev 10
! Generate chain and use autogen to clean up extra dihedrals
! --------------
generate @name2 FIRSt NTER LAST CT3 SETUp

AUTOGEN ANGLes DIHEd

STOP

Re: "FIRST NTER LAST CT3" does NOT work!
jana #3724 10/14/04 07:50 PM
Joined: Sep 2003
Posts: 8,450
rmv Online Content
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It appears to be a bug-- certainly, the "missing" angle parameters are nonsensical, as HA (aliphatic H) is the wrong H atom type for NH3+ (it is HC in the PRES definition for NTER). Also, an H atom shouldn't be the central atom of an angle term, either.

It only seems to break like this for a single amino acid, however; it fails for just Ala, but works fine for Ala-Ala.

Analysis of the NTER and CT3 definitions in the residue topology file (RTF) indicates a probable cause-- the H atoms on both the NH3+ of NTER and the CH3 of CT3 have the same atom names, so there are duplicate HT1, HT2, and HT3 atoms in the same residue as a consequence of the double patch. This is a violation of the RTF rules, and is consistent with most of the "missing parameter" messages as well.

Either use longer peptides (2 or more AA), or else edit one of the PRES definitions to change the H atom names so that they do not conflict.


Rick Venable
computational chemist


Moderated by  John Legato, lennart 

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