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

[Justin Lemkul]

On 8/8/14, 1:58 PM, Dawid das wrote:
> 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?
>

Then you won't have CMAP terms, i.e. you'll basically be reverting back to the 
old CHARMM22 force field.

-Justin

>
> 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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-- 
==================================================

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

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