[gmx-users] MD simulation of Glycoproteion
Dear gromacs users I used Gromacs in order to get a MD simulation of Glycoproteion.now I have got the Glycoproteion's PDB file,When I want to MD by GMX,it gave a Warnning:Fatal error: Residue not found in residue topology database. And I know it was because of the force field,I want to know which force field should be choose in GMX,And where I can get the force field?? Any suggestions? That's all. Thank you-- 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
[gmx-users] Glycoproteion MD
Dear all I am interested in simulating a model of Glycoproteion. I could'nt find the define of the residue in any forcefield .rtp file of GMX. I am using Gromacs 4.5.5 . If any one can help me in getting forcefield parameters for charmm27/ OPLS/Amber99 in gromacs format please respond. Please suggest where else I should search for these. Thanking all-- 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
[gmx-users] MD simulation of Glycoproteion
Dear gromacs users I used Gromacs in order to get a MD simulation of Glycoproteion.now I have got the Glycoproteion's PDB file,When I want to MD by GMX,it gave a Warnning:Fatal error: Residue not found in residue topology database. And I know it was because of the force field,I want to know which force field should be choose in GMX,And where I can get the force field?? Any suggestions? That's all. Thank you-- 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
回复： [gmx-users] MD simulation of Glycoproteion
Thank your advance I have check the residue names, in glyco parts, it contain:NLN,2MA,6MA,WMB,4YB,0YB,XMA,0MA and so on.and I found the define of the residue ,but the format of the define isn't adopt to the Gromacs 's .rtp file. now I don't know how to do it, who can help me? thanking all -- 原始邮件 -- 发件人: Yun Shiyunsh...@gmail.com; 发送时间: 2011年12月15日(星期四) 上午10:48 收件人: Discussion list for GROMACS usersgmx-users@gromacs.org; 主题: Re: [gmx-users] MD simulation of Glycoproteion 2011/12/14 陈应广 525342...@qq.com Dear gromacs users I used Gromacs in order to get a MD simulation of Glycoproteion.now I have got the Glycoproteion's PDB file,When I want to MD by GMX,it gave a Warnning:Fatal error: Residue not found in residue topology database. And I know it was because of the force field,I want to know which force field should be choose in GMX,And where I can get the force field?? Any suggestions? I guess you have to check the residue names, especially those glyco parts, which are probably not in the force field you chose. That's all. Thank you -- 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-- 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
