Re: [gmx-users] How to simulate peptide capped with ACE?
For some reason this didn't send to the mailing list... I use C-terminal amidated peptides, which sounds similar to what you're trying to achieve. Still, more info about what you've done would have made this reply rather shorter. Is the residue still there after pdb2gmx, for instance? I've never seen grompp remove residues, normally, it exits if something is wrong. What I do is: I have a residue in my .rtp for the amino group, and specify the amide as a seperate residue in . When running pdb2gmx, I select the "none" option for that terminus. This works well for me, never seen a problem. Perhaps the format of your ACE entry in your .rtp isn't appropriate... if you're using the preexisting entry, it won't work because there isn't a bond designated to connect it to the backbone (I think). For instance, I have the line: -C N in my [ bonds ] section - check the 3.3 manual, section 5.5.1. - Original Message From: "[EMAIL PROTECTED]" <[EMAIL PROTECTED]> To: gmx-users@gromacs.org Sent: Wednesday, July 11, 2007 2:41:17 PM Subject: [gmx-users] How to simulate peptide capped with ACE? Hi, Mark Thank you for your reply. I¡¯m sorry that I didn¡¯t say my question in detail. I want to simulate the peptide capped with ACE group. I use the ffG43a1 force field. I read some suggestions in mailing list archive and named the residue in the initial structure. I used pdb2gmx and it works well. But when I run grompp, I got the warning ¡± No default G96Angle types, using zeroes.¡±. I check the structure and found that the ACE group disappears. Can you tell me why or how to correct it? Thank you very much! fufeng Liu ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Building a website is a piece of cake. Yahoo! Small Business gives you all the tools to get online. http://smallbusiness.yahoo.com/webhosting ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] How to simulate peptide capped with ACE?
Hi, Mark Thank you for your reply. I¡¯m sorry that I didn¡¯t say my question in detail. I want to simulate the peptide capped with ACE group. I use the ffG43a1 force field. I read some suggestions in mailing list archive and named the residue in the initial structure. I used pdb2gmx and it works well. But when I run grompp, I got the warning ¡± No default G96Angle types, using zeroes.¡±. I check the structure and found that the ACE group disappears. Can you tell me why or how to correct it? Thank you very much! fufeng Liu ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] How to simulate peptide capped with ACE?
[EMAIL PROTECTED] wrote: Dear gromacs users, I trying to simulate a peptide capped with ACE, when I run grompp, I got the following error: WARNING 1 [file "1.top", line 306]: No default G96Angle types, using zeroes. I checked the topology and found the ACE group disappears. I think that the grompp doesn¡¯t handle correctly the ACE group. I had browsed to the mailing list archive and found lots of problems similar to mine, but I couldn¡¯t know how to solve it? Someone can tell me in detail how to do it? No, because you haven't told us what you're trying to do - even what force field you're trying to use. If you're using pdb2gmx, you need to name the residue in the initial structure in a way that allows it to recognise it as ACE, so read ff.rtp and see what acetyl caps get called for force field . Or, read chapter five of the manual and learn how this stuff works!! Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] How to simulate peptide capped with ACE?
Dear gromacs users, I trying to simulate a peptide capped with ACE, when I run grompp, I got the following error: WARNING 1 [file "1.top", line 306]: No default G96Angle types, using zeroes. I checked the topology and found the ACE group disappears. I think that the grompp doesn¡¯t handle correctly the ACE group. I had browsed to the mailing list archive and found lots of problems similar to mine, but I couldn¡¯t know how to solve it? Someone can tell me in detail how to do it? Thank you for your help. Fufeng Liu ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
