[gmx-users] Duplicated dihedral lines on .prm file

[Justin Lemkul]

On 11/9/19 9:30 PM, Daniel Burns wrote:
> Thank you!
>
> Should my ligands have identical names in the .gro file?

For a normal MD simulation, there's no reason to treat the ligands 
differently in any way. You have two copies of the same molecule, so you 
only need one ligand topology and you need to note that there are two of 
these same molecules in the [molecules] directive.

-Justin

>
> On Fri, Nov 8, 2019 at 6:23 PM Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>> On 11/8/19 4:25 PM, Daniel Burns wrote:
>>> Hello,
>>>
>>> I am trying to simulate a dimer with identical ligands bound on each
>>> subunit.
>>>
>>> I generated the ligand files with cgenff.
>>>
>>> I have Liga and Ligb files that each have identical contents (the
>>> filenames, residue, and molecule name are different though).  I am only
>>> getting errors on the Ligb.prm file in the [dihedral types] section.  The
>>> problematic section repeats the i, j, k, and l atoms for 3 or more lines
>>> but each line has different phi and kphi values.  The error is shown
>> below
>>> along with the section of the ligb.prm file that presents the issue.
>>>
>>>
>>> Thank you for your time!
>>>
>>> Dan
>>>
>>> ERROR 9 [file ligb.prm, line 42]:
>>>
>>>     Encountered a second block of parameters for dihedral type 9 for the
>> same
>>>     atoms, with either different parameters and/or the first block has
>>>
>>>     multiple lines. This is not supported.
>>>
>>>
>>> The troublesome lines from ligb.prm:
>>>
>>>
>>> CG2R61   CG2R61    CG321   NG2R51     9     0.000000     0.497896     2
>>>     CG2R61   CG2R61    CG321   NG2R51     9   180.000000     0.552288
>>   4
>>>     CG2R61   CG2R61    CG321   NG2R51     9   180.000000     0.054392
>>   6
>>>     CG2R61    CG321   NG2R51   CG2R51     9     0.000000     1.610840
>>   1
>>>     CG2R61    CG321   NG2R51   CG2R51     9     0.000000     1.757280
>>   2
>>>     CG2R61    CG321   NG2R51   CG2R51     9     0.000000     0.334720
>>   3
>>>     CG2R61    CG321   NG2R51   CG2R51     9     0.000000     0.230120
>>   4
>>>     CG2R61    CG321   NG2R51   NG2R50     9   180.000000     1.610840
>>   1
>>>     CG2R61    CG321   NG2R51   NG2R50     9     0.000000     1.757280
>>   2
>>>     CG2R61    CG321   NG2R51   NG2R50     9   180.000000     0.334720
>>   3
>>>     CG2R61    CG321   NG2R51   NG2R50     9     0.000000     0.230120
>>   4
>>
>> If the ligands are topologically identical, their bonded parameters can
>> only appear once in the topology. You can't simply #include both
>> topologies (despite giving them different [moleculetype] names) because
>> their bonded parameters will be repeated, therefore triggering this error.
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Office: 301 Fralin Hall
>> Lab: 303 Engel Hall
>>
>> Virginia Tech Department of Biochemistry
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalemkul at vt.edu | (540) 231-3129
>> http://www.thelemkullab.com
>>
>> ==================================================
>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>>

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

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================