[gmx-users] Renumber atom ids and charge group in topology (.itp)

[Justin Lemkul]

On 12/16/14 10:16 AM, Nash, Anthony wrote:
> Hi Justin,
>
> If there isn't there isn't. I was just hoping to save myself the effort of correcting for the missing atoms on the crystal structure and the conversion of HIS to HIE/HID with the amber forcefield.
>

In theory, you can certainly write a converter to subtract N atoms from every 
atom number that is found in the topology, but that's a far bigger pain than 
just running through pdb2gmx again, in my mind.

If you had a topology before, why are there missing atom and name issues?

-Justin

> Thanks
> Anthony.
>
> Dr Anthony Nash
> Department of Chemistry
> University College London
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [gromacs.org_gmx-users-bounces at maillist.sys.kth.se] on behalf of Justin Lemkul [jalemkul at vt.edu]
> Sent: 16 December 2014 15:00
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Renumber atom ids and charge group in topology (.itp)
>
> On 12/16/14 9:54 AM, Nash, Anthony wrote:
>> Dear gromacs users,
>>
>> Renumbering the atom ids in a .gro file is very straight forwards, however, after cutting out the first 1/2 of my protein I am having great difficulty aligning my .itp file upon running grompp. Till this stage, it has been far easier for me to remove one particular domain of my protein from my pre-existing .gro file than it would be to adjusting the original crystal structure .pdb file and go through the great pains of getting pdb2gmx to work. But unfortunately I am now left with the fatal error:
>>
>> Atoms in the .top are not numbered consecutively from 1 (rather, atomnr = 2720, while at->nr = 0)
>>
>> which is quite understandable.
>>
>> I discovered an .awk file on the gromacs website. It is approx 5 years old and fails to renumber my atoms in the .itp file correctly. It fails at [ angles ]. I've been 'googling' for a solution but I am yet to find one.
>>
>
> If you're hacking off part of the protein, the most straightforward solution is
> to just regenerate a new topology with pdb2gmx.
>
> -Justin
>
>> All help is appreciated.
>> Thanks
>> Anthony
>>
>> Dr Anthony Nash
>> Department of Chemistry
>> University College London
>>
>
> --
> ==================================================
>
> 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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-- 
==================================================

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

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