Re: [gmx-users] define a new residue
Hi :) I got the parameters of the first 3 residues of the peptide and when I got 0.008e for total charge of the first 2 residues ( formyl and valine). It is expected to be zero. Is the 0.008e acceptable? Or I look for an other way to get the correct parameters and charges? Thaankks! :) Sincerely, Shima From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Monday, July 9, 2012 12:35 AM Subject: Re: [gmx-users] define a new residue On 7/8/12 12:43 PM, Shima Arasteh wrote: OK. What about generating an output file through CGenFF by the first 3 residues of the protein, rather thn the first 2 (formyl+valine)? Maybe. Try it and see, rather than waiting a few hours for someone to get around to replying :) -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 * 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 -- gmx-users mailing listgmx-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
Re: [gmx-users] define a new residue
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 listgmx-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
Re: [gmx-users] define a new residue
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 listgmx-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
Re: [gmx-users] define a new residue
On 7/8/12 7:10 AM, Shima Arasteh wrote: 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 ! Chemically, there is never an H atom on the C-terminal carbonyl of a group involved in a peptide bond. If you parameterized a molecule that was protonated in such a way, it will give an erroneous output. You can't just delete atoms, and shifting the charge by adding it back somewhere else is also very suspect, because you're changing the electronic nature of the compound. I would say you need a better parameterization protocol using a more suitable model compound. -Justin 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: CNC0.3490 ONO-0.4941 H1HC0.1002 NNH1-0.4233 HNH0.094 CACT10.1445 HAHB0.096 CBCT1-0.0977 HBHA0.098 CG1CT3-0.2689 HG11HA0.0910 HG12HA0.0911 HG13HA0.0912 CG2CT3-0.26813 HG21HA0.0914 HG22HA0.0915 HG23HA0.0916 CC0.20917 OO-0.39518 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 listgmx-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 -- 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 listgmx-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
Re: [gmx-users] define a new residue
Thanks all. So if I find a protein which is parametrized by CHARMM and then find the valine residue there, I might use the parameters of side chains of it in my own rtp file. Right? Sincerely, Shima From: francesco oteri francesco.ot...@gmail.com To: jalem...@vt.edu; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Shima Arasteh shima_arasteh2...@yahoo.com Sent: Sunday, July 8, 2012 4:44 PM Subject: Re: [gmx-users] define a new residue Usually in CHARMM the sidechains are parametrized as separate blocks and than merged to the backbone. In fact backbone, in charmm aminoacids, have always tha same charges. So if the same strategy has been used for you residue (you should read the paper reporting the parameterization), you can simply use the standard backbone charges. If this is not the case, You have to develop you charge set. 2012/7/8 Justin A. Lemkul jalem...@vt.edu On 7/8/12 7:10 AM, Shima Arasteh wrote: 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 ! Chemically, there is never an H atom on the C-terminal carbonyl of a group involved in a peptide bond. If you parameterized a molecule that was protonated in such a way, it will give an erroneous output. You can't just delete atoms, and shifting the charge by adding it back somewhere else is also very suspect, because you're changing the electronic nature of the compound. I would say you need a better parameterization protocol using a more suitable model compound. -Justin 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 -0.26813 HG21 HA 0.09 14 HG22 HA 0.09 15 HG23 HA 0.09 16 C C 0.20917 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 -- 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 * Only plain text messages are allowed! * Please search the archive
Re: [gmx-users] define a new residue
On 7/8/12 11:29 AM, Shima Arasteh wrote: Thanks all. So if I find a protein which is parametrized by CHARMM and then find the valine residue there, I might use the parameters of side chains of it in my own rtp file. Right? You can look this up in the force field's .rtp file. For full parameterization procedures, refer to the primary literature for CHARMM. It should detail how to derive parameters for new species. -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 listgmx-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
Re: [gmx-users] define a new residue
OK. What about generating an output file through CGenFF by the first 3 residues of the protein, rather thn the first 2 (formyl+valine)? Sincerely, Shima - Original Message - From: Justin A. Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Sunday, July 8, 2012 9:02 PM Subject: Re: [gmx-users] define a new residue On 7/8/12 11:29 AM, Shima Arasteh wrote: Thanks all. So if I find a protein which is parametrized by CHARMM and then find the valine residue there, I might use the parameters of side chains of it in my own rtp file. Right? You can look this up in the force field's .rtp file. For full parameterization procedures, refer to the primary literature for CHARMM. It should detail how to derive parameters for new species. -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 listgmx-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
Re: [gmx-users] define a new residue
On 7/8/12 12:43 PM, Shima Arasteh wrote: OK. What about generating an output file through CGenFF by the first 3 residues of the protein, rather thn the first 2 (formyl+valine)? Maybe. Try it and see, rather than waiting a few hours for someone to get around to replying :) -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 listgmx-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
Re: [gmx-users] define a new residue
;) Anyway, thanks! Sincerely, Shima - Original Message - From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Monday, July 9, 2012 12:35 AM Subject: Re: [gmx-users] define a new residue On 7/8/12 12:43 PM, Shima Arasteh wrote: OK. What about generating an output file through CGenFF by the first 3 residues of the protein, rather thn the first 2 (formyl+valine)? Maybe. Try it and see, rather than waiting a few hours for someone to get around to replying :) -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 * 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 -- gmx-users mailing listgmx-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
Re: [gmx-users] Define a new residue in oplsaa
Shima Arasteh wrote: Dear GROMACS users, I wanna add add a FOR residue containing atom C and O. In oplsaa force field, the most similar residue to formyl (FOR) is ACE. How I can change the ACE in .rtp file in oplsaa ff to define FOR residue as a new residue? I did like this, Is it correct? No. See below. [ ACE ] [ atoms ] CH3opls_135 -0.180 1 HH31opls_1400.060 1 HH32opls_1400.060 1 HH33opls_1400.060 1 Copls_2350.500 2 Oopls_236 -0.500 2 [ bonds ] CH3 HH31 CH3 HH32 CH3 HH33 CH3 C C O [ impropers ] CH3+NC O improper_O_C_X_Y [ FOR ] [ atoms ] HH31opls_1400.060 1 HH32opls_1400.060 1 HH33opls_1400.060 1 A formyl group has only one H atom, since it is an aldehyde. Copls_2350.500 2 Oopls_236 -0.500 2 The charges here for C, H, and O will likely have to be recalculated. See: http://www.gromacs.org/Documentation/How-tos/Parameterization http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field [ bonds ] C O You need a C-H bond as well. [ impropers ] CH3+NC O improper_O_C_X_Y There is no CH3 in a formyl group. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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 listgmx-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
Re: [gmx-users] Define a new residue in oplsaa
Shima Arasteh wrote: Dear Justin, Thank you so much. Are these changes beneficial for other force fields too? All force fields have to be modified individually and parameters reassigned based on the underlying methodology for parameterization. Thus, the changes you make in OPLS-AA have no use in other force fields. The same strategy is used, of course (per the link on adding residues to a force field), but the parameters that are added will be different in each case. -Justin Cheers, Shima *From:* Justin A. Lemkul jalem...@vt.edu *To:* Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Saturday, April 14, 2012 9:19 PM *Subject:* Re: [gmx-users] Define a new residue in oplsaa Shima Arasteh wrote: Dear GROMACS users, I wanna add add a FOR residue containing atom C and O. In oplsaa force field, the most similar residue to formyl (FOR) is ACE. How I can change the ACE in .rtp file in oplsaa ff to define FOR residue as a new residue? I did like this, Is it correct? No. See below. [ ACE ] [ atoms ] CH3opls_135 -0.1801 HH31opls_1400.0601 HH32opls_1400.0601 HH33opls_1400.0601 Copls_2350.5002 Oopls_236 -0.5002 [ bonds ] CH3 HH31 CH3 HH32 CH3 HH33 CH3C CO [ impropers ] CH3+NC Oimproper_O_C_X_Y [ FOR ] [ atoms ] HH31opls_1400.0601 HH32opls_1400.0601 HH33opls_1400.0601 A formyl group has only one H atom, since it is an aldehyde. Copls_2350.5002 Oopls_236 -0.5002 The charges here for C, H, and O will likely have to be recalculated. See: http://www.gromacs.org/Documentation/How-tos/Parameterization http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field [ bonds ] CO You need a C-H bond as well. [ impropers ] CH3+NC Oimproper_O_C_X_Y There is no CH3 in a formyl group. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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 listgmx-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
Re: [gmx-users] Define a new residue in oplsaa
Thank you so much. Shima From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Saturday, April 14, 2012 9:28 PM Subject: Re: [gmx-users] Define a new residue in oplsaa Shima Arasteh wrote: Dear Justin, Thank you so much. Are these changes beneficial for other force fields too? All force fields have to be modified individually and parameters reassigned based on the underlying methodology for parameterization. Thus, the changes you make in OPLS-AA have no use in other force fields. The same strategy is used, of course (per the link on adding residues to a force field), but the parameters that are added will be different in each case. -Justin Cheers, Shima *From:* Justin A. Lemkul jalem...@vt.edu *To:* Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Saturday, April 14, 2012 9:19 PM *Subject:* Re: [gmx-users] Define a new residue in oplsaa Shima Arasteh wrote: Dear GROMACS users, I wanna add add a FOR residue containing atom C and O. In oplsaa force field, the most similar residue to formyl (FOR) is ACE. How I can change the ACE in .rtp file in oplsaa ff to define FOR residue as a new residue? I did like this, Is it correct? No. See below. [ ACE ] [ atoms ] CH3 opls_135 -0.180 1 HH31 opls_140 0.060 1 HH32 opls_140 0.060 1 HH33 opls_140 0.060 1 C opls_235 0.500 2 O opls_236 -0.500 2 [ bonds ] CH3 HH31 CH3 HH32 CH3 HH33 CH3 C C O [ impropers ] CH3 +N C O improper_O_C_X_Y [ FOR ] [ atoms ] HH31 opls_140 0.060 1 HH32 opls_140 0.060 1 HH33 opls_140 0.060 1 A formyl group has only one H atom, since it is an aldehyde. C opls_235 0.500 2 O opls_236 -0.500 2 The charges here for C, H, and O will likely have to be recalculated. See: http://www.gromacs.org/Documentation/How-tos/Parameterization http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field [ bonds ] C O You need a C-H bond as well. [ impropers ] CH3 +N C O improper_O_C_X_Y There is no CH3 in a formyl group. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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-- gmx-users mailing listgmx-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
