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 <jalem...@vt.edu>:
On 8/8/14, 12:39 PM, Dawid das wrote:
2014-08-08 15:48 GMT+01:00 Justin Lemkul <jalem...@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
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==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
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University of Maryland, Baltimore
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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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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