On 2/14/14, 6:24 PM, Ehsan Sadeghi wrote:
Hi gmx users,
When I run gromacs, there is an issue with the molecules with more than one
residue. for example, for this pdb file:
ATOM 1 C1 VOD 0 8.441 1.158 0.141 1.00 0.00 C
ATOM 2 H1 VOD 0 9.420 1.340 0.570 1.00 0.00 H
ATOM 3 H2 VOD 0 8.580 0.090 0.040 1.00 0.00 H
ATOM 4 H3 VOD 0 8.696 0.757 -0.666 1.00 0.00 H
ATOM 5 C2 VOD 1 7.270 1.800 0.740 1.00 0.00 C
ATOM 6 H4 VOD 1 6.440 1.830 0.030 1.00 0.00 H
ATOM 7 H5 VOD 1 6.950 1.150 1.550 1.00 0.00 H
ATOM 8 O VOD 1 7.640 3.100 1.130 1.00 0.00 O
ATOM 9 H6 VOD 1 8.300 3.360 0.500 1.00 0.00 H
The corresponding residue in aminoacids.rtp is:
[ VOD ]
[ atoms ]
C1 CH2 -0.18000 0
H1 H 0.06000 0
H2 H 0.06000 0
H3 H 0.06000 0
C2 CH3 0.14500 1
H4 H 0.06000 1
H5 H 0.06000 1
O OA -0.68300 1
H6 H 0.41800 1
[ bonds ]
C1 H1 gb_2
C1 H2 gb_2
C1 H3 gb_2
C1 C2 gb_27
C2 H4 gb_2
C2 H5 gb_2
C2 O gb_18
O H6 gb_1
[ angles ]
; ai aj ak gromos type
H1 C1 H2 ga_19
H1 C1 H3 ga_19
H1 C1 C2 ga_19
H2 C1 H3 ga_19
H2 C1 C2 ga_19
H3 C1 C2 ga_19
C1 C2 H4 ga_19
C1 C2 H5 ga_19
C1 C2 O ga_13
H4 C2 H5 ga_19
H4 C2 O ga_30
H5 C2 O ga_30
C2 O H6 ga_30
Problem: When I use pdb2gmx here are the warnings:
-----------------------------------
WARNING: atom C2 is missing in residue VOD 0 in the pdb file
WARNING: atom H4 is missing in residue VOD 0 in the pdb file
WARNING: atom H5 is missing in residue VOD 0 in the pdb file
WARNING: atom O is missing in residue VOD 0 in the pdb file
WARNING: atom H6 is missing in residue VOD 0 in the pdb file
-----------------------
When I combine these 2 residues and make it one, there is no warning. Does
anybody know what is the problem?
Each .rtp entry is a residue. Your coordinate file splits one residue defined
in the .rtp file into two different residues, neither of which matches the .rtp
definition, thus pdb2gmx fails.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
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
==================================================
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
mail to gmx-users-requ...@gromacs.org.
