[gmx-users] Problem with DHT residue not found.

[Justin Lemkul]

On 1/23/16 3:36 AM, Domenico Schitti wrote:
> Hi Tsjerk,
> thank's for you help!
> I followed your instructions (really helpful), then I performed a solvation. When I tried to use "grompp" I got this error:
>
> "number of coordinates in coordinate file (speptideh.gro, 32884)
> does not match topology (speptide.top, 2602)"
>
> I tried to change the x number in the .top file, under [molecules], just at the end of it:
>
> [ molecules ]
> ; Compound        #mols
> Protein_chain_A     1
> DHT                        x
>
> ..But cant fix it.
>

http://www.gromacs.org/Documentation/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology

It's simple to fix.  How many of each species do you have?  That's the number 
that goes in [molecules].  Do you have anything else in the system beyond a 
protein and solvating DHT?  If so, those are missing.

-Justin

> Thank you again!
> Best regards,
> Domenico.
>
>> Date: Sat, 16 Jan 2016 11:30:50 +0100
>> From: tsjerkw at gmail.com
>> To: gmx-users at gromacs.org
>> Subject: Re: [gmx-users] Problem with DHT residue not found.
>>
>> Hi Domenico,
>>
>> - Extract the DHT residue(s) from the PDB file and save it to a separate
>> file (DHT.pdb).
>> - Convert DHT.pdb to DHT.gro
>> - Run pdb2gmx on the protein PDB file; you'll get the GRO and TOP file
>> - Add the coordinates from DHT.gro to the protein GRO file and update the
>> number on the second line of the GRO file (adding the number of atoms from
>> DHT.gro)
>> - Add a line #include "DHT.itp" before the [ system ] directive in the TOP
>> file
>> - Under the [ system ] directive, add DHT with the number of them you have
>> in the GRO file now. Just note that the order of molecules here needs to be
>> the same as the order of molecules in the GRO file.
>>
>> If you need to do this more, I might have an automated workflow taking care
>> of these things...
>>
>> Cheers,
>>
>> Tsjerk
>>
>>
>> On Sat, Jan 16, 2016 at 9:11 AM, Domenico Schitti <dom.90 at hotmail.it> wrote:
>>
>>> Dear Gromacs Users,
>>>
>>> I have to run an md simulation for the 1I37.pdb file, but when I try to
>>> get a topology gromacs give me that error:
>>>
>>> Fatal error:
>>> Residue 'DHT' not found in residue topology database
>>>
>>> So I downloaded a DHT.itp from ATB online but I dont understand how to
>>> properly use it for solve my problem in the fastest way possible.
>>>
>>> I tried to delete all DHT entries from the .pdb file, generating a
>>> topology file.
>>> Then I write #include "dht.itp directory" on the topology made from that
>>> modified pdb file.. But I think thats wrong.
>>>
>>> I read the manual but cant understand well what to do.
>>> Can you please give some suggestions?
>>>
>>> Thank you.
>>>
>>>
>>> Best regards,
>>> Domenico Schitti,
>>> --
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>>
>>
>>
>> --
>> Tsjerk A. Wassenaar, Ph.D.
>> --
>> Gromacs Users mailing list
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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

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