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

[Justin Lemkul]

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
>
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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

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