[gmx-users] No default Ryckaert-Bell. types for proline

[Justin Lemkul]

On 6/3/15 12:00 AM, Kevin C Chan wrote:
> Thanks Justin,
>
> I have long been confused by atom names and types in Gromacs topology. I
> have just went through the manual again, and it confirms me that what we
> read directly in ffbonded.itp under GMXHOME/share/gromacs/top/oplsaa.ff are
> atomtypes. In other words, what you have listed in the last email
>
>    C      CT_2   N      CT_3    3     -5.72371 -18.33847  -5.23419  29.29636
> 0.00000   0.00000 ; Pro (fit to AM1) CD-N-CA-C, JT-R 2/10/97
>    C      CT_2   NT     CT_3    3     -5.72371 -18.33847  -5.23419  29.29636
> 0.00000   0.00000 ; Pro (fit to AM1) CD-N-CA-C, JT-R 2/10/97
>    C_3    CT_2   N      CT_3    3     -5.72371 -18.33847  -5.23419  29.29636
> 0.00000   0.00000 ; Pro COO- terminus.
>    C_3    CT_2   NT     CT_3    3     -5.72371 -18.33847  -5.23419  29.29636
> 0.00000   0.00000 ; Pro COO- terminus.
>
> which was extracted from ffbonded.itp is composed of atomtypes. Meanwhile
> what I have stated in the brackets - (CD N CA C), (CD N CA CB) or (CD N CA
> HA) are by myself read from the topology file after pdb2gmx. To be exact, I
> read
>
> [ dihedrals ]
> ;  ai    aj    ak    al funct            c0            c1            c2
>         c3            c4            c5
>     12     1     4     5     3
>     12     1     4     6     3
>     12     1     4    15     3
>
> ​​
> ​from the topology and refer the numbers (e.g. 12 1 4 15) to the above
> directive ​[ atoms ] to find out that it is (CD N CA C). We can also read
> from directive ​[ atoms ] that under the "type" column, it should be
> (opls_296 opls_309 opls_285 opls_271). So which is the atomtypes, (CD N CA
> C) or (opls_296 opls_309 opls_285 opls_271)? It seems (opls_296 opls_309
> opls_285 opls_271) are the atomtypes, but why the itp states  (C CT_2 N
> CT_3)?
>
> And how can I refer my topology to this line of parameter when it deals (CD
> N CA C) or (opls_296 opls_309 opls_285 opls_271)?
>

Refer to ffnonbonded.itp.  The first column (ignore the fact that it says "name" 
as it is actually a type) is the opls_* atom type for nonbonded interactions, 
the second column is the translated bonded type.  There are fewer bonded types 
(less diversity in interactions) and this convention removes the need for tons 
of redundant parameters.

-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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