On 1/22/13 2:02 PM, Tom wrote:
Thanks a lot, Justin!
I names residue names to match the force field's expectations
But I am still having problem of using amber03.ff.
This my pdb file:
_________
.....
ATOM 28 H5 DC5 1 2.443 -4.389 1.332 1.00 0.00 H
*ATOM 29 P DC 2 7.171 -5.306 6.616 1.00 0.00 P
*
ATOM 30 OP1 DC 2 5.787 -5.066 7.086 1.00 0.00 O
....
__________
When I pdb2gmx, i got Fatal error and choose 1: ( 1: AMBER03 protein, nucleic
AMBER94 (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003))
---------------
Atom P in residue DC 2 was not found in rtp entry*DC5 *with 28 atoms
while sorting atoms.
error report
---------
It seems gmx can not recognize the residue type DC and still used DC5 for
residue 2.
Is there a way to solve this problem?
Please post a link to where the .pdb file can be downloaded.
Also, please do not reply to the entire digest. The archive is already
hopelessly confusing, but let's not make it any worse.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
