On 9/12/13 11:03 AM, Rama Krishna Koppisetti wrote:
Hi,
These are the parameters I kept in the .rtp file for DMPC molecule. Still
getting same error message should I need to look at somewhere else.
[ bondedtypes ]
; Col 1: Type of bond
; Col 2: Type of angles
; Col 3: Type of proper dihedrals
; Col 4: Type of improper dihedrals
; Col 5: Generate all dihedrals if 1, only heavy atoms of 0.
; Col 6: Number of excluded neighbors for nonbonded interactions
; Col 7: Generate 1,4 interactions between pairs of hydrogens if 1
; Col 8: Remove propers over the same bond as an improper if it is 1
; bonds angles dihedrals impropers all_dihedrals nrexcl HH14 RemoveDih
1 1 3 1 1 3 1 0
[ DMPC ]
[ atoms ]
; name type charge chgnr
CN1 LC3 0.4000 1
CN2 LC3 0.4000 1
CN3 LC3 0.4000 1
NTM LNL -0.5000 1
CA LH2 0.3000 1
CB LC2 0.4000 2
OA LOS -0.8000 2
P LP 1.7000 2
OB LOM -0.8000 2
OC LOM -0.8000 2
OD LOS -0.7000 2
[ bonds ]
; ai aj
CN1 NTM
CN2 NTM
CN3 NTM
NTM CA
CA CB
CB OA
OA P
P OB
P OC
P OD
OD CC
CC CD
CD OE
CD CE
OE C1A
If you don't specify bond lengths and force constants here, they need to be
present in ffbonded.itp. Either approach is fine. The only issue you had
before was that you included a function type, which would have explained the
error you got before.
[ angles ]
; ai aj ak funct angle fc
CN1 NTM CN2 2 109.50 520.00
CN1 NTM CN3 2 109.50 520.00
CN1 NTM CA 2 109.50 520.00
CN2 NTM CN3 2 109.50 520.00
CN2 NTM CA 2 109.50 520.00
CN3 NTM CA 2 109.50 520.00
NTM CA CB 2 111.00 530.00
CA CB OA 2 111.00 530.00
CB OA P 2 120.00 530.00
OA P OC 2 109.60 450.00
OA P OB 2 109.60 450.00
OA P OD 2 103.00 420.00
P OD CC 2 120.00 530.00
OC P OB 2 120.00 780.00
OC P OD 2 109.60 450.00
Same as with [bonds], you cannot have a function type specified here.
[ dihedrals ]
; ai aj ak al funct ph0 cp mult
CN3 NTM CA CB 1 0.00 3.77 3
NTM CA CB OA 1 0.00 8.62 3
CA CB OA P 1 0.00 3.77 3
CB OA P OD 1 0.00 3.19 3
OA P OD CC 1 0.00 3.19 3
P OD CC CD 1 0.00 3.77 3
OD CC CD CE 1 0.00 5.92 3
CC CD OE C1A 1 0.00 3.77 3
CC CD CE OG 1 0.00 5.92 3
CD OE C1A C1B 1 180.00 24.00 2
CD CE OG C2A 1 0.00 3.77 3
OE C1A C1B C1C 1 0.00 1.00 6
[ impropers ]
; GROMOS improper dihedrals
; ai aj ak al funct angle fc
CD OE CE CC 2 35.26 334.72
C1A OE OF C1B 2 0.00 167.36
C2A OG OH C2B 2 0.00 167.36
Same applies for the dihedrals and impropers.
To avoid another string of incomplete replies, please answer the following
questions directly. Remember, I'm trying (very hard) to help you resolve this
and we're just spinning our wheels.
1. Did you re-run pdb2gmx after modifying the .rtp file?
2. Have you looked into the [bonds] directive in the .top file that pdb2gmx
created to see if anything is out of place? Every line should have 5 entries:
atom_i atom_j funct b0 kb
Anything more or less (in this case) is wrong. Can you identify any problematic
lines, and if so, to which atoms do they apply?
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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