On 9/2/13 12:59 PM, Golshan Hejazi wrote:
Hello,
I am trying to add ethanol as a new residue to CGenFF force field in gromacs.
Basically, I need to bring this information from charmm rtf file to the gromacs
format. This is the information taken from rtf file of charmm.
RESI ETOH 0.00 ! C2H6O Ethanol, adm jr.
GROUP
ATOM C1 CG321 0.05 ! H21 H11 H12
ATOM O1 OG311 -0.65 ! \ \ /
ATOM HO1 HGP1 0.42 ! H22--C2--C1
ATOM H11 HGA2 0.09 ! / \
ATOM H12 HGA2 0.09 ! H23 O1--HO1
GROUP
ATOM C2 CG331 -0.27
ATOM H21 HGA3 0.09
ATOM H22 HGA3 0.09
ATOM H23 HGA3 0.09
BOND C1 C2 C1 O1 C1 H11 C1 H12 O1 HO1
BOND C2 H21 C2 H22 C2 H23
DONO HO1 O1
ACCE O1
! for ic build
IC O1 C1 C2 H21 0.0000 0.0000 180.0000 0.0000 0.0000
IC C1 H21 *C2 H22 0.0000 0.0000 120.0000 0.0000 0.0000
IC C1 H21 *C2 H23 0.0000 0.0000 240.0000 0.0000 0.0000
IC O1 C2 *C1 H11 0.0000 0.0000 240.0000 0.0000 0.0000
IC O1 C2 *C1 H12 0.0000 0.0000 120.0000 0.0000 0.0000
IC C2 C1 O1 HO1 0.0000 0.0000 180.0000 0.0000 0.0000
I have added The ATOM and BOND information to the aminoacid.rtp file.
I thought that the rest of the information are optional and pdb2gmx doesn't
complain while generating the topology. But when I use the topology and gro
file to do a minimization. The molecule bonds break apart and what I see is an
exploded molecule.
Please post your complete .rtp entry and the contents of the resulting .top
file.
So I thought probably the rest of the information are important too, for
example:
DONO HO1 O1
ACCE O1
But I dont know where to put them.
These lines are only used by CHARMM during hydrogen bond analysis or in the
archaic form that included a hydrogen bonding term to the energy function.
-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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