On 5/23/17 2:16 PM, Mohammad Hassan Khatami wrote:
Thank Justin!
I finished adding the new “residues” in the .rtp file. pdb2gmx runs straight
forward. However, while doing energy minimizations, I get several errors like
the ones below, arise:
ERROR 2 [file topol.top, line 396]:
No default U-B types
and
ERROR 5 [file topol.top, line 550]:
No default Proper Dih. types
As it says, they might be related to the angles and dihedral parameters. Do you
have any suggestion on where (and how) to add them?
You shouldn't need to add parameters, but without knowing what is on those lines
(more specifically, the associated atom types because the atom numbers will mean
nothing to me) there's nothing else I can say about it. The entirety of the
carbohydrate force field should already be ported over, so missing parameters
are very odd.
-Justin
Thanks again,
MH
On 5/22/17 1:09 AM, Mohammad Hassan Khatami wrote:
Hi Justin,
I am asked to focus on learning how to change and update the CHARMM36
parameters, so I could implement the future changes and patches easier. (Thus,
I am not focused in the Glycan Reader, at the moment.)
Thank you! I think I now have a better understanding of what should I do. For
each part of my polymer,i.e. the initial, the middle and the final part, I have
to modify the AGLC molecule to represent each of these parts, seperately.
So, lets say to introduce the 1->4 linkage, I need to to apply 14ba patch from
the top_all36_carb.rtf into the merged.rtp file of GROMACS CHARMM36. In this case,
I need to create a new version of [ AGLC ] molecule (lets call it [ AGLC14 ]) in
the merged.rtp, with the changes below from the the top_all36_carb.rtf, applied to
it:
Note that your residue name must be limited to 4 characters so it can properly
be read from the input coordinates. AGLC14 won't work.
! equatorial-axial 1->4 linkage
PRES 14ba 0.02 ! (i)1->4(i-1) equatorial at C1 and axial at C4
dele atom 1HO4
dele atom 2HO1
dele atom 2O1
ATOM 1C4 CC3161 0.09 !
ATOM 1O4 OC301 -0.36 !
ATOM 2C1 CC3162 0.29 !
BOND 1O4 2C1
I have to remove the HO4, HO1 and O1 lines and modify the values for the C4, O4
and C1 atoms. Then, I need to add the bond of
[ bond ]
…
O4 +C1
Correct.
Then, I need to apply the bonds and angles parameters in the the
top_all36_carb.rtf (below), into the merged.vsd file of the GROMACS CHARMM36.
! I J K L R(IK) T(IKJ) PHI T(JKL) R(KL)
IC 1C3 1C4 1O4 2C1 1.5071 110.40 -86.30 121.00 1.3902 ! psi
IC 1C4 1O4 2C1 2O5 1.4560 121.00 -130.97 108.63 1.4470 ! phi
IC 2O5 1O4 *2C1 2C2 1.4470 108.63 -122.09 110.89 1.5316
IC 2O5 1O4 *2C1 2H1 1.4470 108.63 121.92 111.32 1.0837
I have figured out how to implement R(IK), T(IKJ), T(JKL) and R(KL) values into
the merged.vsd file, except for the PHI values. Where (and/or how) should I put
it?
Am I on the right track?
You should not do this. The .vsd file is for defining virtual sites. The IC
lines are for the CHARMM program's internal coordinate builder, specifying some
optimized geometry (one that the force field in total should produce, or come
very close). All the bonded parameters you need are already in the force field
because they come from the corresponding .prm files. Do not adjust bonded
parameter files.
-Justin
Thanks again for your help.
MH
On May 19, 2017, at 5:36 PM, Justin Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
On 5/19/17 9:57 AM, Mohammad Hassan Khatami wrote:
First, I am looking for 1->4 and 1->6 linkages. In the top_all36_carb.rtf file
I found different linkages for beta-glucose, but non for alpha-glucose.
I am trying to make a simple chain with 1->4 linkages like below:
alpha-D-glucose,1->4,alpha-D-glucose,1->4,alpha-D-glucose,1->4,alpha-D-glucose.
Linkages are not specific to the sugar; most are totally generic. A few
comments suggest specific usage and may be corner cases, but your patches will
be among 14aa, 14ab, 14ba, 14bb.
Then, I might need to branch them with1->6 linkage.
Also totally possible.
I tried Glycan Reader, but itstill crashes.
Uploading a correctly named PDB file should work in Glycan Reader or the Quick MD
Simulator, but "still crashes" is not diagnostic of anything. Specific help
with CHARMM-GUI should be brought to their attention, though.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
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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