[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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