[gmx-users] adding ETHANOL to CGennFF in gromacs has problem

[Justin Lemkul]

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

-- 
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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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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