On 9/12/13 9:21 AM, Rama Krishna Koppisetti wrote:
Hi
[ 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 ]
; ai Ber_type charge chgnr mass
CN1 LC3 0.4000 1 15.0350
CN2 LC3 0.4000 1 15.0350
CN3 LC3 0.4000 1 15.0350
NTM LNL -0.5000 1 14.0067
CA LH2 0.3000 1 14.0270
CB LC2 0.4000 2 14.0270
OA LOS -0.8000 2 15.9994
P LP 1.7000 2 30.9738
OB LOM -0.8000 2 15.9994
OC LOM -0.8000 2 15.9994
OD LOS -0.7000 2 15.9994
CC LC2 0.4000 3 14.0270
CD LH1 0.3000 3 13.0190
Now I'm trying to execute command to get ions.tpr file
grompp -f minim.mdp -c conf_solv.gro -p topol.top -o ions.tpr
Error encountered was:
------------------------------
------------------------
Program g_grompp, VERSION 4.5.5
Source code file: /builddir/build/BUILD/gromacs-4.5.5/src/kernel/toppush.c,
line: 1631
Fatal error:
Incorrect number of parameters - found 3, expected 2 or 4 for Bond.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
Given that it's the same error as before, either (1) you didn't fix the bonded
directives within [DMPC] (not shown above) or (2) you did not re-create the
topology with the corrected .rtp file. Remember that the contents of an .rtp
file are irrelevant once pdb2gmx is done.
-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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