From: surya narayanan chandrasekaran (sonofsunsurya_at_gmail.com)
Date: Thu Nov 01 2018 - 23:45:39 CDT

Hi,
    I was trying to build a simulation box containing individual amino
acid. So here is what i did and tried. First i got for eg HIS pdb and
genereated usign packmol a box of 25 HIS individual units and tried to
generate psf using psf plugin i see a bond connecting NTER and CTER. Which
i dont want. So i included TER at the end of each unit of my pdb and
generated it then also i got the same. So i extracted the top file for HSD
and replaced N and C parts with NTER and CTER and tried to build the pdb
still its not helpful bcoz i was not able to sort out IC (internal coord)
in topology file[ i hope there lies my problem]. So if anyone gives a idea
how i can create psf without creating bonds between N and CTER it will be
helpful. So basically HIS units are far apart and sp NTER and CTER has long
distance units.

DECL -CA
DECL -C
DECL -O
DECL +N
DECL +HN
DECL +CA
AUTO ANGLES DIHE

RESI HSD 0.00 ! neutral HIS, proton on ND1
GROUP
ATOM N NH3 -0.30 !
ATOM HT1 HC 0.33 ! HT1
ATOM HT2 HC 0.33 ! (+)/
ATOM HT3 HC 0.33 ! --CA--N--HT2
ATOM CA CT1 0.21 ! | \
ATOM HA HB 0.10 ! HA HT3
!ATOM N NH1 -0.47 ! | HD1 HE1
!ATOM HN H 0.31 ! HN-N | /
!ATOM CA CT1 0.07 ! | HB1 ND1--CE1
!ATOM HA HB 0.09 ! | | / ||
GROUP ! HA-CA--CB--CG ||
ATOM CB CT2 -0.09 ! | | \\ ||
ATOM HB1 HA 0.09 ! | HB2 CD2--NE2
ATOM HB2 HA 0.09 ! O=C |
ATOM ND1 NR1 -0.36 ! | HD2
ATOM HD1 H 0.32
ATOM CG CPH1 -0.05
GROUP
ATOM CE1 CPH2 0.25
ATOM HE1 HR1 0.13
ATOM NE2 NR2 -0.70
ATOM CD2 CPH1 0.22
ATOM HD2 HR3 0.10
GROUP ! use in generate statement
ATOM C CC 0.34 ! OT2(-)
ATOM OT1 OC -0.67 ! /
ATOM OT2 OC -0.67 ! -C
!DELETE ATOM O ! \\
!DELETE ATOM HN ! OT1
BOND HT1 N HT2 N HT3 N
BOND CB CA CG CB ND1 CG CE1 ND1
BOND NE2 CD2 N HN N CA
BOND C CA CA HA CB HB1
BOND CB HB2 ND1 HD1 CD2 HD2 CE1 HE1
BOND C OT2
DOUBLE C OT1
DOUBLE CG CD2 CE1 NE2
!IMPR OT1 CA OT2 C
IMPR C CA OT2 OT1
IMPR ND1 CG CE1 HD1 CD2 CG NE2 HD2 CE1 ND1 NE2 HE1
IMPR ND1 CE1 CG HD1 CD2 NE2 CG HD2 CE1 NE2 ND1 HE1
!IMPR N -C CA HN C CA +N O
!DONOR HN N
DONOR HD1 ND1
DONOR HT1 N
DONOR HT2 N
DONOR HT3 N
ACCEPTOR NE2
!ACCEPTOR O C
ACCEPTOR OT1 C
ACCEPTOR OT2 C
!IC -C CA *N HN 1.3475 123.2700 180.0000 115.2100 0.9988
!IC -C N CA C 1.3475 123.2700 180.0000 107.7000 1.5166
!IC N CA C +N 1.4521 107.7000 180.0000 117.5700 1.3509
!IC +N CA *C O 1.3509 117.5700 180.0000 120.2400 1.2273
IC CA C +N +CA 1.5166 117.5700 180.0000 123.7200 1.4545
!IC N C *CA CB 1.4521 107.7000 122.4600 109.9900 1.5519
!IC N C *CA HA 1.4521 107.7000 -117.4900 107.3700 1.0830
IC N CA CB CG 1.4521 112.1200 180.0000 114.0500 1.5041
IC CG CA *CB HB1 1.5041 114.0500 121.1700 109.0100 1.1118
IC CG CA *CB HB2 1.5041 114.0500 -122.3600 109.5300 1.1121
IC CA CB CG ND1 1.5519 114.0500 90.0000 124.1000 1.3783
IC ND1 CB *CG CD2 1.3783 124.1000 -171.2900 129.6000 1.3597
IC CB CG ND1 CE1 1.5041 124.1000 -173.2100 107.0300 1.3549
IC CB CG CD2 NE2 1.5041 129.6000 171.9900 110.0300 1.3817
IC NE2 ND1 *CE1 HE1 1.3166 111.6300 -179.6300 123.8900 1.0932
IC CE1 CG *ND1 HD1 1.3549 107.0300 -174.6500 126.2600 1.0005
IC NE2 CG *CD2 HD2 1.3817 110.0300 -177.8500 129.6300 1.0834

IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000
IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000
IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000
IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000
IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000

END

-- 
Warm regards,
Dr. Suryanarayanan C