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 -- 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
