[gmx-users] Pull code grompp error

[Justin Lemkul]

On 3/24/17 11:18 AM, Souparno Adhikary wrote:
> Hi Kausar,
>
> I tried it with an index file. It seemed to run fine but did not produce
> any "pull" i.e. shifting away of the DNA molecule from the protein. I used
> a harmonic potential. And also, why do I need to specify the index file
> when, according to the error itself, it can be run without making an index
> file, just putting the name of the molecules?
>

GROMACS has certain default groups that include anything specified as a 
[moleculetype] name.  Anything else has to be formed as an index group.

-Justin

> Thanks,
>
> Souparno
>
> On Fri, Mar 24, 2017 at 1:03 PM, Tasneem Kausar <tasneemkausar12 at gmail.com>
> wrote:
>
>> Define you pull group in index file  as the error message says.
>>
>> On Fri, Mar 24, 2017 at 12:18 PM, Souparno Adhikary <souparnoa91 at gmail.com
>>>
>> wrote:
>>
>>> Hi,
>>>
>>> Below is my .mdp code for pulling as found in the tutorial by Justin
>>> Lemkul. I made the required changes to match my version syntax.
>>>
>>> pull                    = umbrella
>>> pull_ngroups            = 2
>>> pull_group0        = Protein_chain_A
>>> pull_group1        = DNA_chain_B
>>> pull_group2        = DNA_chain_C
>>> pull_geometry    = distance      ; simple distance increase
>>> pull_dim         = Y N N
>>> pull_rate1        = 0.01          ; 0.01 nm per ps = 10 nm per ns
>>> pull_rate2        = 0.01
>>> pull_k1           = 1000          ; kJ mol^-1 nm^-2
>>> pull_k2           = 1000
>>> pull_start       = yes           ; define initial COM distance > 0
>>>
>>> When I tried to grompp using this code, it generates an error:
>>>
>>> Fatal error:
>>> Group topol_Protein_chain_A referenced in the .mdp file was not found in
>>> the index file.
>>> Group names must match either [moleculetype] names or custom index group
>>> names, in which case you must supply an index file to the '-n' option
>>> of grompp.
>>>
>>> I searched for the solutions in the Gromacs forum and found it might be
>> due
>>> to name mismatch. But, in my case, the names are exactly same as
>> referenced
>>> in the *.mdp file. Below is the molecule names from the topol.top file.
>>>
>>> [ molecules ]
>>> ; Compound        #mols
>>> Protein_chain_A     1
>>> DNA_chain_B         1
>>> DNA_chain_C         1
>>> SOL         33542
>>> NA               125
>>> CL               98
>>>
>>> Can you please help to solve the problem? I tried with changing the names
>>> to Protein and DNA (the residue types) and changing the ngroups to 3.
>>> Nothing worked.
>>>
>>> Regards,
>>>
>>> Souparno Adhikary
>>> University of Calcutta,
>>> India.
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-- 
==================================================

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

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