[gmx-users] New residue in FF does not bond to others.

[Dawid das]

Thank you but now I have different type of question.
If I use -nocmap option for pdb2gmx what impact on the result of my
simulation?


2014-08-08 19:42 GMT+01:00 Justin Lemkul <jalemkul at vt.edu>:

>
>
> On 8/8/14, 12:39 PM, Dawid das wrote:
>
>> 2014-08-08 15:48 GMT+01:00 Justin Lemkul <jalemkul at vt.edu>:
>>
>>  The problem is in atom naming.  You have used MN1 and MC3 for the
>>> equivalent of amino acid N and C atoms, respectively.  pdb2gmx chokes
>>> here,
>>> because Phe-65 tries to make a bond to the +N atom, which it does not
>>> find
>>> until it runs into Ser-69.  Likewise with the C atom in CH6.  If you
>>> rename
>>> these atoms (MN1->N, MC3->C) in the .rtp and .hdb, everything works fine.
>>>
>>>
>> OK, I see your point but if I do as you suggest how will I specify
>> nonbonding parameters in ffnonbonded.itp? What I mean is that MN1 and MC3
>> atoms have different  vdW and electrostatic parameters than N and C atoms,
>> respectively.
>>
>>
> Realize that atom *names* and atom *types* are separate entities.  You
> have all your names and types the same, which can be confusing.  All you
> need to do is *name* the atom N and assign it a *type* of MNH1 or whatever
> it was.  Parameters are always assigned by type, not name.
>
>
>
>>
>>  If there are still missing parameters for interactions, you'll have to
>>> figure that out.  There are several missing inter-residue angles and
>>> dihedrals in your .rtp entry for CH6.
>>>
>>>
>> Do you mean those which I stated above?
>>
>>
> Above?  You mean in a previous message?  Most of those errors were derived
> from incorrect, nonsensical bonding.
>
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> 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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