[gmx-users] alamethicin error

[pragya chohan]

----------------------------------------> Date: Fri, 2 Nov 2007 09:39:36 +1100> From: Mark.Abraham at anu.edu.au> To: gmx-users at gromacs.org> Subject: Re: [gmx-users] alamethicin error>> pragya chohan wrote:>> i got this error "atom C not found in residue 84PHL while combining tdb and rtp" when i tried to do pdb2gmx>> the commamd used is:>> pdb2gmx -ter -ff gmx -f alamethicin.pdb -o alamethicin.gro -p ala.top>> There's a warning given by pdb2gmx about this forcefield. You would do> well to read it.>>> Select N-terminus type (start)>> 0: NH3+>> 1: NH2>> 2: None>> 2>> N-terminus: None>> Select C-terminus type (end)>> 0: COO->> 1: COOH>> 2: None>> 1>> C-terminus: COOH>> even if i use option 0 i get an the same error. But if i ued option 2 in C-terminali get :>> Atom C not found in residue 21 while adding improper... which is also PHL>> 84PHL is>> ATOM 655 N PHL 84 42.380 33.130 47.420 1.00 0.00>> ATOM 656 H PHL 84 41.620 33.340 46.800 1.00 0.00>> ATOM 657 CA PHL 84 43.050 34.310 47.980 1.00 0.00>> ATOM 658 CB PHL 84 43.960 34.910 46.910 1.00 0.00>> ATOM 659 CG PHL 84 45.060 33.960 46.410 1.00 0.00>> ATOM 660 CD1 PHL 84 46.080 33.540 47.290 1.00 0.00>> ATOM 661 HD1 PHL 84 46.090 33.860 48.320 1.00 0.00>> ATOM 662 CD2 PHL 84 45.040 33.520 45.070 1.00 0.00>> ATOM 663 HD2 PHL 84 44.280 33.880 44.390 1.00 0.00>> ATOM 664 CE1 PHL 84 47.080 32.660 46.830 1.00 0.00>> ATOM 665 HE1 PHL 84 47.870 32.330 47.480 1.00 0.00>> ATOM 666 CE2 PHL 84 46.040 32.650 44.600 1.00 0.00>> ATOM 667 HE2 PHL 84 46.050 32.350 43.570 1.00 0.00>> ATOM 668 CZ PHL 84 47.050 32.220 45.490 1.00 0.00>> ATOM 669 HZ PHL 84 47.830 31.570 45.140 1.00 0.00>> ATOM 670 CX PHL 84 41.990 35.310 48.450 1.00 0.00>> ATOM 671 OY PHL 84 40.950 34.570 49.110 1.00 0.00>> ATOM 672 HY PHL 84 40.110 35.090 49.220 1.00 0.00>> So, what important part of an amino *acid* residue is missing from this> fragment?>> Mark> _______________________________________________> gmx-users mailing list gmx-users at 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 gmx-users-request at gromacs.org.> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Thanks Mark. The C terminal does not have a -COOH group at the end but rater has a -OH group.... PHL is actually PHENYLALANINOL.
But when i put option 2 whn prompted for 
select C-terminus type (end)>> 0: COO->> 1: COOH>> 2: None 
 i still get an error Atom C not found in residue 21 while adding improper.
I checked the naming in ffgmx.rtp but everything seems to be fine. 
Thanks for your help.

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