[gmx-users] Problem in .gro file

[faride badalkhani]

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.

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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