On 5/19/15 2:45 PM, Andrew Bostick wrote:
Dear Justin
Based on your answer (You don't want to be adding 2 HZ here, just one
since it is a peptide bond.), I modified LYS2 in aminoacids.hdb file
LYS2 2
1 1 H N -C CA
1 4 HZ NZ CE CD
But, after pdb2gmx, I encountered with
WARNING: atom HZ1 is missing in residue LYS 540 in the pdb file
You might need to add atom HZ1 to the hydrogen database of
building block LYS2
in the file aminoacids.hdb (see the manual)
WARNING: atom HZ2 is missing in residue LYS 540 in the pdb file
You might need to add atom HZ2 to the hydrogen database of
building block LYS2
in the file aminoacids.hdb (see the manual).
What is the reason of this issue? Is there problem in my rtp file (about
LYS2 and GLU2 entries)?
Yes. This:
[ LYS2 ]
[ atoms ]
N N -0.28000 0
H H 0.28000 0
CA CH1 0.00000 1
CB CH2 0.00000 1
CG CH2 0.00000 2
CD CH2 0.00000 2
CE CH2 0.00000 2
NZ NT -0.28000 3
HZ1 H 0.28000 3
HZ2 H 0.00000 3
Here, you specify two HZ atoms, when you actually only want one (look at the
structure of a peptide bond!). The .hdb entry specifies one HZ to be built
(with the name HZ), but your .rtp tells pdb2gmx there should be two, HZ1 and
HZ2. That, of course, is not correct, as is assigning a zero charge to any H
atom here.
-Justin
C C 0.380 4
O O -0.380 4
[ bonds ]
N H gb_2
N CA gb_20
CA C gb_26
C O gb_4
C +N gb_9
CA CB gb_26
CB CG gb_26
CG CD gb_26
CD CE gb_26
CE NZ gb_20
NZ HZ1 gb_2
NZ HZ2 gb_2
[ angles ]
; ai aj ak gromos type
-C N H ga_31
H N CA ga_17
-C N CA ga_30
N CA C ga_12
CA C +N ga_18
CA C O ga_29
O C +N ga_32
N CA CB ga_12
C CA CB ga_12
CA CB CG ga_14
CB CG CD ga_14
CG CD CE ga_14
CD CE NZ ga_14
CE NZ HZ1 ga_10
CE NZ HZ2 ga_10
HZ1 NZ HZ2 ga_9
[ impropers ]
; ai aj ak al gromos type
N -C CA H gi_1
C CA +N O gi_1
CA N C CB gi_2
[ dihedrals ]
; ai aj ak al gromos type
-CA -C N CA gd_4
-C N CA C gd_19
N CA C +N gd_20
N CA CB CG gd_17
CA CB CG CD gd_17
CB CG CD CE gd_17
CG CD CE NZ gd_17
CD CE NZ HZ1 gd_14
Thanks in advance.
--
==================================================
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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