[gmx-users] OPLS force field issue....

Justin Lemkul jalemkul at vt.edu
Wed Jan 22 22:21:14 CET 2014



On 1/22/14, 4:03 PM, Sidath Wijesinghe wrote:
> 1. could you please tell me what does this mean ? " charge group is
> inappropriately large"  the overall charge is appear to zero in my topology. i
> am little confused here.
>

Manual section 3.4.2.  If you are using the Verlet cutoff scheme, it's not 
relevant, but if you are using the group scheme, it is critical to get the 
charge groups right or else the neighbor searching is totally broken.

> 2. if below atoms types in  represent C 1&11...so on  and those atom types
> appear in the error....
>
> C    opls_240    0    12.011    3    C 0.142   C 0.142   C 0.142
> C    opls_239    0    12.011    2    C 0.142   C 0.142 and if i cannot see these
> lines in  ffnonbonded.itp
> do i need to add them in ffnonbonded.itp?
>

You do not need to modify ffnonbonded.itp.  The modifications belong in 
ffbonded.itp or the topology itself.  The complication with OPLS-AA is that 
there are "nonbonded atom types" and "bonded atom types."  In ffnonbonded.itp, 
the first column is the nonbonded type and the second column is the bonded type, 
which is used in ffbonded.itp.  You will need to do some mapping between your 
atoms and their types to figure out which sequences of atom types have undefined 
dihedrals.  Those need to be added in [ dihedraltypes ] of ffbonded.itp or in 
the .top file directly.

-Justin

>
> On Wed, Jan 22, 2014 at 2:20 PM, Justin Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
>     On 1/22/14, 1:06 PM, Sidath Wijesinghe wrote:
>
>            Justin,
>
>         i was able to generate  the .top file for 3 monomers by making the
>         corresponding
>         .rtp entry.
>
>         below   is a segment of my .rtp entry and thr .pdb file i used.
>
>         .rtp entry for first few atoms out of 208
>
>         [ UNK ]
>            [ atoms ]
>
>         C1      opls_240        0       1
>         C2      opls_145        -0.12   1
>         C3      opls_240        0       1
>         C4      opls_240        0       1
>         C5      opls_158        -0.12   1
>         C6      opls_158        -0.12   1
>         C7      opls_158        -0.12   1
>         C8      opls_158        -0.12   1
>         C9      opls_158        -0.12   1
>         C10     opls_158        -0.12   1
>
>
>     I can almost guarantee that charge group is inappropriately large.  Charge
>     groups generally have no more than 3-4 atoms (see the manual).
>
>
>            [ bonds ]
>         C1      C2
>         C1      C13
>         C1      C82
>         C2      C3
>         C2      H28
>         C3      C4
>         C3      C5
>         C4      C11
>         C4      C21
>         C5      C6
>         C5      H29
>
>         and so on....
>
>         segment of my .pdb used.
>         ATOM      1 C1    UNK     1     -0.3884 0.71623 0.01741  1.00  0.00      UNK
>         ATOM      2 C2    UNK     1     0.52009 1.96858 0.02142  1.00  0.00      UNK
>         ATOM      3 C3    UNK     1     2.05261  1.8016 0.02832  1.00  0.00      UNK
>         ATOM      4 C4    UNK     1     2.67378 0.39693 0.04493  1.00  0.00      UNK
>         ATOM      5 C5    UNK     1     3.00381 3.01293 0.02021  1.00  0.00      UNK
>         ATOM      6 C6    UNK     1     2.43967 4.44371 0.06547  1.00  0.00      UNK
>         ATOM      7 C7    UNK     1     3.74954 5.25409 0.04830  1.00  0.00      UNK
>         ATOM      8 C8    UNK     1     3.66193 6.78984 0.08175  1.00  0.00      UNK
>         ATOM      9 C9    UNK     1     5.14612 7.20376 0.05800  1.00  0.00      UNK
>         ATOM     10 C10   UNK     1     5.41193  8.7194 0.08617  1.00  0.00      UNK
>         ATOM     11 C11   UNK     1     4.20533 0.24061 0.06162  1.00  0.00      UNK
>         ATOM     12 C12   UNK     1     5.73704 0.08685 0.07550  1.00  0.00      UNK
>         ATOM     13 C13   UNK     1     0.24354 -0.6927 0.01957  1.00  0.00      UNK
>         ATOM     14 C14   UNK     1     -0.6215 -1.9681 0.00425  1.00  0.00      UNK
>         ATOM     15 C15   UNK     1     -2.1484 -1.7855 0.06322  1.00  0.00      UNK
>
>
>         i was able to get the .gro and .top file using pdb2gmx
>
>         after that i was using grompp but i got an error message as follows.
>
>         ERROR 254 [file topol.top, line 1941]:
>             No default Ryckaert-Bell. types
>
>
>         ERROR 255 [file topol.top, line 1942]:
>             No default Ryckaert-Bell. types
>
>
>         ERROR 256 [file topol.top, line 1943]:
>             No default Ryckaert-Bell. types
>         i was reading the gmx_users blogs and it specifies that i need to
>         manually enter
>         the parameters that have errors.
>
>         i am not clear with that. could you please tell me what i need to do here. (
>         when i look the lines regarding the errors  they
>         are pointing out the diheadrals)
>
>
>     You need to check those lines for what the atom types are for those atoms.
>     Parameters are not present in ffbonded.itp for that sequence of atoms so you
>     need to add suitable parameters.
>
>
>     -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
>
>     jalemkul at outerbanks.umaryland.__edu
>     <mailto:jalemkul at outerbanks.umaryland.edu> | (410) 706-7441
>     <tel:%28410%29%20706-7441>
>
>     ==============================__====================
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>
>
>
> --
> Sidath Wijesinghe
> Graduate Teaching Assistant
> Dept Of Chemistry
> Clemson University
>

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

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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