[gmx-users] Problem in .gro file

[Justin Lemkul]

On 6/29/15 8:34 AM, faride badalkhani wrote:
> At first I created a copy of GROMOS 53A6 in a folder. Then, I made some
> changes in files as follows:
> 1. I defined atom types that weren't included in .atp file, and removed all
> other atom types that I didn't need.
> 2. I included all bonds, angles, and dihedrals of the residues in
> ffbonded.itp, and removed all other gb_, ga_, and gd_ types that I didn't
> need.
> 3. I made the changes were needed in ffnonbonded.itp
> 4. I defined 3 new residues in .rtp file
> 5. Finally, I included the new FF in forcefield.itp file
>
> I haven't done anything with specbond. dat yet.
>

OK, so how about sharing your input and output coordinates?  The preparation of 
the topology and interpretation of the coordinates are separate issues.

-Justin

> Truly yours,
> Farideh
>
> On Mon, Jun 29, 2015 at 4:39 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 6/29/15 8:07 AM, faride badalkhani wrote:
>>
>>> Thanks for answer, but when use a visualization software for .pdb file, it
>>> looks correct. All atoms are in the correct position.
>>> what about specbonds.dat? Could you tell me if it can help in my case?
>>>
>>>
>> All I can do is guess randomly and that's not productive.  Please provide
>> a full description of what you did to prepare the topology, any .rtp or
>> specbond.dat modifications, and upload your input and output coordinate
>> files somewhere.
>>
>> -Justin
>>
>>
>>
>>> On Mon, Jun 29, 2015 at 4:32 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>>
>>>
>>>>
>>>> On 6/29/15 8:00 AM, faride badalkhani wrote:
>>>>
>>>>   Dear all,
>>>>>
>>>>> I am trying to simulate a hyperbranced polymer (a dendrimer) with
>>>>> gromacs.
>>>>> Therefore, I have parametrized the GROMOS 53A6 FF, and executed pdb2gmx,
>>>>> and got a command as follows:
>>>>> "You have successfully generated a topology from : G3-Neutral.pdb
>>>>> The Pamam force field and the spce water model are used."
>>>>>
>>>>> But, when I open the G3-Neutral_processed.gro with VMD, it is in a
>>>>> strange
>>>>> shape, and hasnt got the correct form af a dendrimer. It seems that it
>>>>> annot realize the correct connections between residues in a branched
>>>>> polymar such as dendrimer.
>>>>>
>>>>>
>>>>>   The bonds you see in a visualization software are guessed based on
>>>> distances and have nothing to do with the topology, which is definitive.
>>>>
>>>> Probably your input PDB file is misformatted such that the coordinates
>>>> are
>>>> misinterpreted by pdb2gmx.  The file format is fixed, so any shifting of
>>>> columns causes junk to be produced.
>>>>
>>>> -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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>> --
>> ==================================================
>>
>> 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
>>
>> ==================================================
>> --
>> Gromacs Users mailing list
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>> * Please search the archive at
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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

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