[gmx-users] dihedral restraints

[Jessica Leuchter]

To get the dihedrals to stay restrained to their original values what
should the kfac be?

On Fri, Mar 20, 2015 at 3:04 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 3/20/15 9:00 AM, Jessica Leuchter wrote:
>
>> Dear All,
>>
>> I would like to add dihedral restraints to 10 residues in my topology
>> file using the newest version of gromacs.  I have done the
>> following(see below) to my topology file. And this is the *grompp
>> command* I am using: gmx grompp -f ions.mdp -c 1AKI_solv.gro -p
>> topol.top -o ions.tpr. But I am getting the error message below.
>>
>> *topol.top file*:
>>
>> [ dihedral_restraints ]
>> ;  ai       aj    ak      al        fnID    phi    dphi    kfac
>>
>>   1497  1499  1509  1511     9    -70.488     0       1
>>   1499  1509  1511  1513     9    -12.561     0       1
>>   1511  1513  1515  1518     9     95.706     0       1
>>   1513  1515  1518  1520     9   -117.614     0       1
>>   1518  1520  1522  1530     9   -111.163     0       1
>>   1520  1522  1530  1532     9    -72.034     0       1
>>   1530  1532  1534  1542     9   -108.627     0       1
>>   1532  1534  1542  1544     9   -103.437     0       1
>>   1542  1544  1554  1556     9    -80.981     0       1
>>   1544  1554  1556  1558     9     46.231     0       1
>>   1556  1558  1560  1570     9   -107.016     0       1
>>   1558  1560  1570  1572     9     20.452     0       1
>>   1570  1572  1574  1587     9    -82.626     0       1
>>   1572  1574  1587  1589     9    169.300     0       1
>>   1587  1589  1591  1608     9    -82.868     0       1
>>   1589  1591  1608  1610     9    -47.555     0       1
>>   1608  1610  1612  1623     9    -39.285     0       1
>>   1610  1612  1623  1625     9    -72.644     0       1
>>   1623  1625  1627  1642     9     -7.261     0       1
>>   1625  1627  1642  1644     9    -51.880     0       1
>>   1642  1644  1646  1652     9    -38.845     0       1
>>   1644  1646  1652  1654     9    -73.856     0       1
>>
>>
>> *Fatal error:*
>> Incorrect number of parameters - found 2, expected 3 or 6 for Dih. Rest..
>> For more information and tips for troubleshooting, please check the
>> GROMACS
>> website at http://www.gromacs.org/Documentation/Errors
>>
>>
> Your restraints directive uses the wrong format.  See manual section
> 5.7.1, which has a complete example of dihedral restraints and an
> explanation of all the required columns.
>
> -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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-- 
Jessica Leuchter
Wake Forest University 2014
954.591.2222