[gmx-users] add a group to an amino acid

Hi, I'm using the OPLS force field. [ PHE ] [ atoms ] Nopls_238 -0.500 1 Hopls_2410.300 1 CAopls_224B 0.140 1 HAopls_1400.060 1 CBopls_149 -0.005 2 HB1opls_1400.060 2 HB2opls_1400.060 2

Re: [gmx-users] add a group to an amino acid

: ../../../../src/kernel/add_par.c, line: 233 Fatal error: Atom HB11 not found in rtp database in residue BOC, it looks a bit like HB1 --- ... What should i do? On Sun, Nov 7, 2010 at 4:49 PM, Justin A. Lemkul jalem...@vt.edu wrote: hengame fallah wrote

Re: [gmx-users] add a group to an amino acid

CZCl CG2 HG1 CG2 HG2 CG2 C C O -C N and still i got that error! Fatal error: Atom HB11 not found in rtp database in residue BOC, it looks a bit like HB1 On Tue, Nov 9, 2010 at 1:12 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 9/11/2010 8:19 PM, hengame

Re: [gmx-users] add a group to an amino acid

CD2 HD2 CD2 CE2 CE1 HE1 CE1CZ CE2 HE2 CE2CZ CZHZ C O -C N and i got the charges by Gaussian. I'm very confused now [?] On Tue, Nov 9, 2010 at 2:13 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 9/11/2010 9:09 PM, hengame fallah wrote

Re: [gmx-users] add a group to an amino acid

Dear Mark, I think that i couldn't explain my problem clearly, however i have changed my .rtp but i don't know how should be my .hdb file. a) The structure of *BOC* is: *-CO-CH2-CH(C6H5Cl)-CH2-NH-* b) This is the new charges: [ BOC ] [ atoms ] Nopls_238 -0.500 1 H

Re: [gmx-users] add a group to an amino acid

I read about .hdb file and then i editted my .hdb file: ... BOC 9 11H N -CCA 26HA CA N CB 15HB CB CA CG1CG2 11HD1CD1CG1CE1 11HD2CD2CG1CE2 11HE1CE1CD1CZ 1

Re: [gmx-users] add a group to an amino acid

Thank you very much, Mark! The problem was for the type CG2 in .rtp. I corrected it and the errors disappear.[?] (I should study more for that non-zero charge, i think.) 332.gif-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the

[gmx-users] tfe.gro

Hi, Does anyone have the tfe.gro for solvent box? I have the tfe.itp file in /usr/share/gromacs/top/ directory. [ atoms ] 1 C 1 TFE C 1 0.74 2 F 1 TFE F 1-0.25 3 F 1 TFE F

Re: [gmx-users] tfe.gro

Thank you very much ABEL Stephane. On Tue, Nov 30, 2010 at 3:28 PM, ABEL Stephane 175950 stephane.a...@cea.frwrote: Hi Hengameh Below, my TFE.gro (with the atom names for CHARMM Cgenff) i used it previously for md. You can easely translated in others ff you use 9 1TFE O11