CHARMM Development Project Forums CHARMM Community Bug Reports & Fixes "FIRST NTER LAST CT3" does NOT work!

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

Here is the input file you can use to test:
* 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

the problem is due to atom names in NTER and CT3 being the same (HT1 and so on) combined with the use of those two patches with the same residue number. the fix is to simply change the name of the HT1, HT2 and HT3 atoms in CT3, as follows.

alex

PRES CT3b 0.00 ! N-Methylamide C-terminus
GROUP ! use in generate statement
ATOM C C 0.51 !
ATOM O O -0.51 ! |
GROUP ! C=O
ATOM NT NH1 -0.47 ! |
ATOM HNT H 0.31 ! NT-HNT
ATOM CAT CT3 -0.11 ! |
ATOM HT1b HA 0.09 ! HT1-CAT-HT3
ATOM HT2b HA 0.09 ! |
ATOM HT3b HA 0.09 ! HT2
!
BOND C NT NT HNT NT CAT CAT HT1b CAT HT2b CAT HT3b
DIHE CA C NT CAT
IMPR NT C CAT HNT C CA NT O
DONOR HNT NT
IC N CA C O 0.0000 0.0000 180.0000 0.0000 0.0000
IC NT CA *C O 0.0000 0.0000 180.0000 0.0000 0.0000
IC C CAT *NT HNT 0.0000 0.0000 180.0000 0.0000 0.0000
IC CA C NT CAT 0.0000 0.0000 180.0000 0.0000 0.0000
IC C NT CAT HT1b 0.0000 0.0000 60.0000 0.0000 0.0000
IC C NT CAT HT2b 0.0000 0.0000 180.0000 0.0000 0.0000
IC C NT CAT HT3b 0.0000 0.0000 -60.0000 0.0000 0.0000