[gmx-users] OPLS force field issue....
Sidath Wijesinghe
swijesi at g.clemson.edu
Tue Feb 4 04:14:38 CET 2014
Justin,,
i rechecked the opls/ff that i used and found some errors, after correction
them i got the .top file.
note that i was able to define the charge groups as well. when i use this
.top file with grompp,
now am getting 12 errors...as follwos..
ERROR 1 [file topol.top, line 1399]:
No default Ryckaert-Bell. types
ERROR 2 [file topol.top, line 1400]:
No default Ryckaert-Bell. types
ERROR 3 [file topol.top, line 1415]:
No default Ryckaert-Bell. types
ERROR 4 [file topol.top, line 1416]:
No default Ryckaert-Bell. types
and so on...
i did the mapping as you suggested,as an example line 1399 in .top
as follwos...
2 1 82 81 3 ( here 2 1 82 & 81 are carbon atoms)
and the mapping to all 12 errors.....then modified the ffbonded.itp file's
diheadral block as follows...
C2 C1 C82 C81 3 0.00 0.00 0.00 0.00
so on....
then bond tyype block as follows....
C2 C1 1 0.00 0.00... so on....
added those atom types in atomtypes.atp like below...
C1
C2
C3
C4
C11
C12
C13................so on
after that when i do grompp gives me a fatal error like
Program grompp, VERSION 4.5.5
Source code file: toppush.c, line: 631
Fatal error:
Unknown bond_atomtype C1
could you please tell me what i have done wrong?
and at the same time....i tied delete those 12 lines in .top and do
grompp...it worked....but when i
did mdrun.....i am getting the signs of blowing up system....what i can do
over here....how can i get rid of these errors
and carry out my simulation?
Thank you!
Sidath
On Wed, Jan 22, 2014 at 4:19 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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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> Gromacs Users mailing list
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--
Sidath Wijesinghe
Graduate Teaching Assistant
Dept Of Chemistry
Clemson University
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