Because I saw that residues defined in aminoacids.rtp file don't have H in their carboxyl and atom N. So I decided to remove H !
Sincerely, Shima ________________________________ From: francesco oteri <francesco.ot...@gmail.com> To: Shima Arasteh <shima_arasteh2...@yahoo.com> Cc: Discussion list for GROMACS users <gmx-users@gromacs.org> Sent: Sunday, July 8, 2012 3:28 PM Subject: Re: [gmx-users] define a new residue Why have you removed the hydrogen? 2012/7/8 Shima Arasteh <shima_arasteh2...@yahoo.com> Dear Francesco, >Thanks. Honestly I thought about this, but I don't know how much charges I >need to increase or decrease of other atoms? > >Is it possible to add the FVAL with the H atom( which I removed before)? I >mean that I apply the complete formyl-valine and don't remove the H atom. > >Thanks for your suggestions. > > >Cheers, >Shima > > > >________________________________ >From: francesco oteri <francesco.ot...@gmail.com> >To: Shima Arasteh <shima_arasteh2...@yahoo.com>; Discussion list for GROMACS >users <gmx-users@gromacs.org> >Sent: Sunday, July 8, 2012 3:04 PM >Subject: Re: [gmx-users] define a new residue > > > >Hi Shima, >usually charge calculation are carried out on the system that is supposed to >be used in the MD. >So in my opinion you shouldn't remove the hydrogen. >Anyway, if you wanna remove the hydrogen, either you increase the charge of >some other atom or >calculate the charges on the new residue without hydrogen. > >Francesco > > >2012/7/8 Shima Arasteh <shima_arasteh2...@yahoo.com> > >Hi dear gmx friends, >> >>I got the parameters of formyl-valine through the CHARMM website. Now I need >>to define it as a new residue FVAL( as Justin suggested me earlier) in .rtp >>file. To set the correct charges for atoms, I used the CHARMM output. In >>order to define FVAL to rtp file, I added these lines as below: >> >>CN C 0.349 0 >> ON O -0.494 1 >> H1 HC 0.100 2 >> N NH1 -0.423 3 >> HN H 0.09 4 >> CA CT1 0.144 5 >> HA HB 0.09 6 >> CB CT1 -0.097 7 >> HB HA 0.09 8 >> CG1 CT3 -0.268 9 >> HG11 HA 0.09 10 >> HG12 HA 0.09 11 >> HG13 HA 0.09 12 >> CG2 CT3 -0.268 13 >> HG21 HA 0.09 14 >> HG22 HA 0.09 15 >> HG23 HA 0.09 16 >> C C 0.209 17 >> O O -0.395 18 >> >>As you see I omitted the H connected to Carboxyl. Now the total charge of the >>new-defined residue is not zero (-0.333) . How can I correct it? >> >> >>I would appreciate you for your suggestions. >>Thanks in advance. >> >>Sincerely, >>Shima >>-- >>gmx-users mailing list gmx-users@gromacs.org >>http://lists.gromacs.org/mailman/listinfo/gmx-users >>* Only plain text messages are allowed! >>* 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 >> > > >-- >Cordiali saluti, Dr.Oteri Francesco > -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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