[gmx-users] force field problem....

[Kamalesh Roy]

Hi Justin
Thank you, for the help....I have made topology from PRODRG server and then
manually edited
as required...but the column gromos type is unknown unlike other molecule
in the ff..
Where do I get this?

Kamalesh..



On Thu, Apr 16, 2015 at 7:04 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 4/16/15 9:09 AM, Ming Tang wrote:
>
>> Hi, Justin
>> Thank you so much. I should be much more cautious in the future.
>> there is another interesting thing. why doesn't it give the warning
>> regarding mismatching between CLA and CL when I use MG in the pdb and topol
>> file?
>>
>
> There is no connection between the force field and this issue.  I can
> offer no explanation other than to tell you something else is going on
> there that you didn't account for.
>
>  I did not copy CN88. actually, I typed it. I got those 2 parameters from
>> oplsaa. I found that in ffnanonbonded.itp in charmm27.ff, MG and CAL in
>> different types of pairs has the same sigma1-4 and epsilon 1-4, so I give
>> SR the same as well.
>>
>>
> Don't mix and match force fields.  This is fundamentally unsound.
> Specific pair interactions (1-4) or nonbonded interactions (NBFIX) are
> highly tuned for specific interactions.  Don't make any assumptions based
> on things that "look similar."
>
> -Justin
>
>
>  Sent from my Huawei Mobile
>>
>> Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>
>> On 4/16/15 7:12 AM, Kamalesh Roy wrote:
>>
>>> Dear all,
>>>
>>> please suggest for the topology for oleic acid..
>>> The information retreived after we run editconf...
>>>
>>> as a result atoms of the molecule becoming non bonded......in the box..
>>>
>>>
>> editconf doesn't add or remove bonds.  What you see in VMD (or whatever)
>> is not
>> necessarily true (only the topology is definitive), but if the geometry
>> is bad
>> then you'll get weird-looking states.  Your input coordinates could be
>> messed up
>> somehow.
>>
>>  8 out of 8 lines of specbond.dat converted successfully
>>> Checking for duplicate atoms....
>>> Generating any missing hydrogen atoms and/or adding termini.
>>> Now there are 1 residues with 20 atoms
>>> Making bonds...
>>> No bonds
>>> Generating angles, dihedrals and pairs...
>>> Making cmap torsions...There are    0 dihedrals,    0 impropers,    0
>>> angles
>>>                0 pairs,        0 bonds and     0 virtual sites
>>>
>>
>> Your .rtp entry is faulty if this is the outcome.
>>
>> -Justin
>>
>>  Total mass 279.445 a.m.u.
>>> Total charge -1.000 e
>>> Writing topology
>>>
>>> Back Off! I just backed up oleic1.itp to ./#oleic1.itp.1#
>>>
>>>
>> --
>> ==================================================
>>
>> 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 http://www.gromacs.org/
>> Support/Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>>
>>
> --
> ==================================================
>
> 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 http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>