Re: [AMBER] problem in writing pdb with ambpdb

From: Jio M <>
Date: Mon, 19 Dec 2011 04:55:36 -0800 (PST)


(thanks to Pavan, Marc and Astrid and all)

>> have you tried the "-aatm" option with ambpdb?

yes your suggestion is WORKING!!!. I get correct pdb now. But as Marc (Dr. or Prof. sorry I dont know) suggested I tried with ptraj which writes wrong atom name in pdb. This means ptraj is not able to detect correct atom names and so it will not be able to do analysis correctly or not at all.

So is there any option like -aatm (for ambpdb) in ptraj so that it can read correct names if I want to use, e.g., mask options?? if not then I have to modify my main prep file.

thanks and regards;


 From: Astrid Maaß <>
To: Jio M <>; AMBER Mailing List <>
Sent: Monday, December 19, 2011 5:44 PM
Subject: Re: [AMBER] problem in writing pdb with ambpdb
Hi Jiom,

have you tried the "-aatm" option with ambpdb? This helped me once.


----- Ursprüngliche Mail -----
Von: "Jio M" <>
An: "amber" <>
Gesendet: Montag, 19. Dezember 2011 11:38:53
Betreff: [AMBER] problem in writing pdb with ambpdb

Dear All;

I am using prep file and created prmtop file and inpcrd. Job runs smoothly. Now when I wanted to save pdb using ambpdb the atom names in pdb are not printed correctly. My prep file has many atoms having four letters (like C218), which are obviously printed in prmtop file also. but while writing pdb file from prmtop file and restart file ambpdb gets confused. But TOP2MOL2 works fine.

e.g. here are prmtop some lines:

H12RH12SC211H11RH11SC210H101C29 H91 C28 H8R H8S C27 H7R H7S C26 H6R H6S C25 H5R
H5S C24 H4R H4S C23 H3R H3S C22 H2R H2S C21 O22 O21 C2  C1  O11 P   O13 O14 O12

Actually names are C218 H18R H18S H18S and so on...

but pdb (from ambpdb) write names as RH18 SH18, but top2mol2 is working OK.

So I have following queries:

1) is this prmtop correct? and does this 4 letter name will give wrong results with ptraj for analysis??

2) if prmtop is correct please someone suggest how I can write correct atom name pdb??? or I should modify names in prep file itself by reducing 4 letter/character atom name to 2 or 3 letters??

thanks and regards;
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Received on Mon Dec 19 2011 - 05:00:02 PST
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