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

[Justin Lemkul]

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
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University of Maryland, Baltimore
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Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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