[gmx-users] Problem in .gro file

[faride badalkhani]

I cannot understand what do you mean with input and output coordinates?
I have attached the .gro, posre.itp and topol.top files.
Could you help me please with this one?

Truly yours,
Farideh

On Tue, Jun 30, 2015 at 12:22 PM, faride badalkhani <
farideh.khamseh at gmail.com> wrote:

> I cannot understand what do you mean with input and output coordinates?
> I have attached the .pdb, .gro, posre.itp and topol.top files.
> Could you help me please with this one?
>
> Truly yours,
> Farideh
>
> On Mon, Jun 29, 2015 at 7:38 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> 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
>>>>
>>>> * 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
>>
>> ==================================================
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
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>> posting!
>>
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>
>