[gmx-users] ffbond.itp

[Justin Lemkul]

On 2/23/15 1:04 AM, marzieh dehghan wrote:
> Hi every body
>
>
> 1-      In the phosphate group, we have 4 oxygen atoms that bond to the
> phosphate. Two of them are as follow: CH2-O-P-OH and the others include:
>
> -          A double bond is on the top of phosphor atom
>
> -          A OH group is at the bottom of phosphor atom
>
> We put the atom type of OH group as OA, but We would like to know atom type
> of each oxygen bounded to phosphate group. Because we cannot decide between
> OA (hydroxyl, sugar or ester oxygen) and OM (carboxyl oxygen).
>

OM.  See ATP as an example in the .rtp file.

> 2-      If we can't find dihedral parameters of covalent bond for
> ffbound.itp, please let us know, can we left blank it?
> we are looking forward to getting your nice answer
>

Simply leaving it out is a very poor idea.  You can't just ignore hard problems 
:)  Dihedrals are not compulsory, in theory, because they are really just 
correction factors for imbalances in nonbonded interactions, so most 1-4 
interactions require dihedrals.  Phosphates are particularly important, because 
there can be considerable electrostatic attraction or repulsion with neighboring 
groups.

-Justin

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

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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