Re: [gmx-users] Fatal error: In the chosen force field there is no residue type for 'GLN' as a starting terminus
On 2012-11-18 10:40, Atila Petrosian wrote: Dear David Thanks for your attention. I have 2 problems/questions: 1) There are a specific orientation for GLN ligand with regard to protein in my system. If I do what you said [you make a separate molecule Gln-Ala using pymol or vmd], specific orientation for GLN ligand with regard to protein are changed. no since you only use the procedure for the topology creation. 2) topology obtained from NGLN-CALA is as follows: [ moleculetype ] ; Namenrexcl Protein 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeBchargeB massB ; residue 1 GLN rtp NGLN q +1.0 1 N3 1GLN N 1 0.1493 14.01 ; qtot 0.1493 2 H 1GLN H1 2 0.1996 1.008 ; qtot 0.3489 3 H 1GLN H2 3 0.1996 1.008 ; qtot 0.5485 4 H 1GLN H3 4 0.1996 1.008 ; qtot 0.7481 5 CT 1GLN CA 5 0.0536 12.01 ; qtot 0.8017 6 HP 1GLN HA 6 0.1015 1.008 ; qtot 0.9032 7 CT 1GLN CB 7 0.0651 12.01 ; qtot 0.9683 8 HC 1GLNHB1 8 0.005 1.008 ; qtot 0.9733 9 HC 1GLNHB2 9 0.005 1.008 ; qtot 0.9783 10 CT 1GLN CG 10-0.0903 12.01 ; qtot 0.888 11 HC 1GLNHG1 11 0.0331 1.008 ; qtot 0.9211 12 HC 1GLNHG2 12 0.0331 1.008 ; qtot 0.9542 13 C 1GLN CD 13 0.7354 12.01 ; qtot 1.69 14 O 1GLNOE1 14-0.6133 16 ; qtot 1.076 15 N 1GLNNE2 15-1.0031 14.01 ; qtot 0.0732 16 H 1GLN HE21 16 0.4429 1.008 ; qtot 0.5161 17 H 1GLN HE22 17 0.4429 1.008 ; qtot 0.959 18 C 1GLN C 18 0.6123 12.01 ; qtot 1.571 19 O 1GLN O 19-0.5713 16 ; qtot 1 ; residue 2 ALA rtp CALA q -1.0 20 N 2ALA N 20-0.3821 14.01 ; qtot 0.6179 21 H 2ALA H 21 0.2681 1.008 ; qtot 0.886 22 CT 2ALA CA 22-0.1747 12.01 ; qtot 0.7113 23 H1 2ALA HA 23 0.1067 1.008 ; qtot 0.818 24 CT 2ALA CB 24-0.2093 12.01 ; qtot 0.6087 25 HC 2ALAHB1 25 0.0764 1.008 ; qtot 0.6851 26 HC 2ALAHB2 26 0.0764 1.008 ; qtot 0.7615 27 HC 2ALAHB3 27 0.0764 1.008 ; qtot 0.8379 28 C 2ALA C 28 0.7731 12.01 ; qtot 1.611 29 O2 2ALAOC1 29-0.8055 16 ; qtot 0.8055 30 O2 2ALAOC2 30-0.8055 16 ; qtot 0 You said Then you edit the top file (remove superfluous alanine atoms, rename the N in ALA to O2 etc) with a text editor until it is correct with help from the rtp file for CGLN. You may have to smooth the charges to keep it neutral In ALA residue, all atoms except for N are redundant atoms. After removing them and renaming N in ALA to O2, what remains in top file? Both of NGLN and CALA or only NGLN? If latter is true, [ atoms ] ; nr type resnr residue atom cgnr charge mass typeBchargeB massB ; residue 1 GLN rtp GLN q 0.0 1 N3 1GLN N 1 0.1493 14.01 ; qtot 0.1493 2 H 1GLN H1 2 0.1996 1.008 ; qtot 0.3489 3 H 1GLN H2 3 0.1996 1.008 ; qtot 0.5485 4 H 1GLN H3 4 0.1996 1.008 ; qtot 0.7481 5 CT 1GLN CA 5 0.0536 12.01 ; qtot 0.8017 6 HP 1GLN HA 6 0.1015 1.008 ; qtot 0.9032 7 CT 1GLN CB 7 0.0651 12.01 ; qtot 0.9683 8 HC 1GLNHB1 8 0.005 1.008 ; qtot 0.9733 9 HC 1GLNHB2 9 0.005 1.008 ; qtot 0.9783 10 CT 1GLN CG 10-0.0903 12.01 ; qtot 0.888 11 HC 1GLNHG1 11 0.0331 1.008 ; qtot 0.9211 12 HC 1GLNHG2 12 0.0331 1.008 ; qtot 0.9542 13 C 1GLN CD 13 0.7354 12.01 ; qtot 1.69 14 O 1GLNOE1 14-0.6133 16 ; qtot
Re: [gmx-users] Fatal error: In the chosen force field there is no residue type for 'GLN' as a starting terminus
On 2012-11-17 15:37, Atila Petrosian wrote: Hi all. After using amber03 force field for protein-ligand simulation (pdb2gmx), I encountered with following error: Fatal error: In the chosen force field there is no residue type for 'GLN' as a starting terminus. Ligand in my system is a single residue (GLN). There are [GLN], [NGLN] and [CGLN] in rtp file of amber03 force field. Should this single residue be as both of [NGLN] and [CGLN]? How to fix this error? Any help will highly appreciated. Manually making a toplogy is your best best. Add an alanine after the gln then in the top file rename and remove atoms. GAFF is an alternative but it will not give you exactly the same charges and LJ parameters. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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] Fatal error: In the chosen force field there is no residue type for 'GLN' as a starting terminus
On 2012-11-17 16:26, Atila Petrosian wrote: Dear David Thanks for your quick reply. You said Add an alanine after the gln then in the top file rename and remove atoms. I confused. Why ALA? ALA (alanine) is a residue which is very simple than GLN structurally. I should add alanine after the gln. But in which file? you make a separate molecule Gln-Ala using pymol or vmd and then run it through pdb2gmx, this will give you NGLN-CALA. Then you edit the top file (remove superfluous alanine atoms, rename the N in ALA to O2 etc) with a text editor until it is correct with help from the rtp file for CGLN. You may have to smooth the charges to keep it neutral. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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
