Dear All, The protein on which I am working, have few ASN residues which are N-linked with the N-acetyl-glucosamine (NAG). I have taken the parameters of the NAG and N-linked ASN from the GLYCAM_06. I have added this N-linked ASN as a new residue in aminoacids.rtp file and accordingly all the parametrs are added in respective files. After this both pdb2gmx and grompp are working without any error.
But the problem I am facing is related to 1-4 scaling. For the GLYCAM, fudgeLJ and fudgeQQ should be 1. I have read the following mailing post that how one can mix the fudgeLJ and fudgeQQ in GROMACS. http://lists.gromacs.org/pipermail/gmx-users/2011-April/060839.html In the manual, I have come across with two type of pairs function. In function type 1, two parameters are needed and is used as default. But, in function type 2, five parameters are needed: fudgeQQ, q_i, q_j, V(cr) and W(cr). So can I replace function type 1 with 2 in the pdb2gmx generated topology for only those pairs belong to the NAG and side chains of N-linked ASN. So that, I can use fudgeQQ of 1.0, q_i / q_j from the rtp/topology and V(cr) / W(cr) (calculated from the sigma and epsilon using combination rule) for those pairs. Will this give No Scaling for 1-4 pair belong to NAG and side chains of N-linked ASN. Or another which I found “those 1-4 pairs belong to side chains of N-linked ASN and NAG, so I could remove them from [ pairs ] section and put into the [ pairs_nb ] section.” Then these pairs will be treated as normal non-bonded pairs. Please suggest me, what I can do in this regard and which is the correct way. Thank you in advance. -- With Regards, Rashmi Kumari Research Scholar School of Computational and Integrative Sciences Jawaharlal Nehru University New Delhi- 110067.
-- 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
