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

[Dawid das]

Very well. Thank you for your assistance :).


2014-08-08 21:00 GMT+01:00 Justin Lemkul <jalemkul at vt.edu>:

>
>
> 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
>
> ==================================================
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> Gromacs Users mailing list
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