On 3/6/17 10:23 AM, Urszula Uciechowska wrote:
Hi,
I do not know. After running pdb2gmx I am not getting the .itp file for
the DC5... I am using gromacs 5.0.4. What can be wrong here?
Did you check the .rtp for DC5, as Mark suggested? Based on your knowledge of
DNA structure, why might there be an issue with a 5'-phosphorus atom?
-Justin
Urszula
Hi,
What name does the .rtp entry for DC5 use for its phosphorus atom?
Mark
On Mon, Mar 6, 2017 at 1:39 PM Urszula Uciechowska <
urszula.uciechow...@biotech.ug.edu.pl> wrote:
Dear gmx users,
After running a pdb2gmx script of the pdb file I am getting an error
message:
Fatal error:
Atom P in residue DC 2 was not found in rtp entry DC5 with 28 atoms
while sorting atoms.
The DC 2 in pdb file:
TER 11412 LEU B 366
ATOM 11413 P DC C 2 0.997 17.702 5.368 1.00 77.21
P
ATOM 11414 OP1 DC C 2 -0.278 17.623 4.612 1.00 76.82
O
ATOM 11415 OP2 DC C 2 1.374 16.596 6.287 1.00 76.77
O
ATOM 11416 O5' DC C 2 2.181 17.899 4.319 1.00 75.66
O
ATOM 11417 C5' DC C 2 2.302 19.107 3.565 1.00 72.46
C
What can be wrong with the P atom?
Thanks for any suggestions.
best
Urszula Uciechowska
-----------------------------------------
Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego
http://www.ug.edu.pl/
--
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.
--
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.
--------------------------------------------
Urszula Uciechowska PhD
University of Gdansk and Medical Univesity of Gdansk
Department of Molecular and Cellular Biology
ul. Abrahama 58
80-307 Gdańsk
Poland
-----------------------------------------
Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego
http://www.ug.edu.pl/
--
==================================================
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
==================================================
--
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.
