[gmx-users] Structure breaking during minimization

[Justin Lemkul]

On 10/27/16 8:06 AM, Apramita Chand wrote:
> Dear Justin,
> My .rtp entry for taurine is
> [TAU]
>   [ atoms ]
>       O3    OM   -0.607     1
>       S1    SDmso 0.849     1
>       O1    OM   -0.607     1
>       O2    OM   -0.607     1
>       C2    CH2  -0.039     2
>       C1    CH2   0.376     2
>       N1    NL   -0.469     3
>       H5    H     0.368     3
>       H6    H     0.368     3
>       H7    H     0.368     3
>    [ bonds ]
>       OM    SDmso   gb_25
>       SDmso CH2     gb_32
>       CH2   CH2     gb_26
>       NL    H       gb_2
>    [ angles]
>      OM   SDmso  CH2   ga_46
>      SDmso CH2   CH2   ga_16
>      CH2   NL    H     ga_11
>      H     NL    H     ga_10
>
> Why does it break during minimization? The .pdb file was downloaded from
> ATB server and charges have been assigned from the .itp file .
>
> What could be wrong?

Bonds and angles have to be assigned by name, not type.  Your structure 
effectively specifies no bonds at all.

-Justin

> If I optimize a structure using Gaussian and use that structure and charges
> for running in GROMOS53a6 ff , should I make an rtp file and assign atom
> types,bond types from GROMOS ff which seem to match with my actual
> structure . What is the procedure here?
>
>
> Regards,
> Apramita
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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