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

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

On 16/11/2010 9:04 PM, hengame fallah wrote: Thank you very much, Mark! Now i have errors from my .top file after grompp command. The question is that why in pdb2gmx, editconf ,genbox and make_ndx steps i don't see these errors: ... processing topology... Opening library file

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

On 14/11/2010 7:26 PM, hengame fallah wrote: 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-* Great. b) This is the new charges: [ BOC ]

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

On 14/11/2010 8:13 PM, hengame fallah wrote: I read about .hdb file and then i editted my .hdb file: ... BOC 9 Then you'll know from your reading what this number should be :-) It's the number of types of hydrogen atoms that might be added. For each of them, there's one line below. You

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

Thanks Justin, actually the protein that i want to simulate consists of two amino acids: PHE and BOC BOC is an unusual amino acid as you know. It has a Cl instead of HZ in PHE and has one extra CH2 in comparison to PHE I finally defined a residue BOC in opls .rtp file: [ BOC ] [ atoms ] N

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

On 9/11/2010 8:19 PM, hengame fallah wrote: Thanks Justin, actually the protein that i want to simulate consists of two amino acids: PHE and BOC BOC is an unusual amino acid as you know. It has a Cl instead of HZ in PHE and has one extra CH2 in comparison to PHE So that probably means

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

Dear Mark, I edited my pdb like this: ... ATOM 41 N BOC 3 -1.862 5.210 5.333 ATOM 42 H BOC 3 -2.325 4.344 5.618 ATOM 43 CA BOC 3 -1.001 5.232 4.169 ATOM 44 HA1 BOC 3 -0.540 6.235 4.026 ATOM 45 HA2 BOC 3

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

On 9/11/2010 9:09 PM, hengame fallah wrote: Dear Mark, I edited my pdb like this: ... ATOM 41 N BOC 3 -1.862 5.210 5.333 ATOM 42 H BOC 3 -2.325 4.344 5.618 ATOM 43 CA BOC 3 -1.001 5.232 4.169 ATOM 44 HA1 BOC 3 -0.540

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

This is .rtp for [PHE] in opls: [ 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 CG

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

On 9/11/2010 10:10 PM, hengame fallah wrote: This is .rtp for [PHE] in opls: ...wherein all the charge groups are neutral, unlike yours for BOC. This will be fairly moot for a PME simulation, however. [ PHE ] [ atoms ] N opls_238

[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

hengame fallah wrote: 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 HB2